1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
5 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
7 ;;; This file is part of GNU Guix.
9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
10 ;;; under the terms of the GNU General Public License as published by
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12 ;;; your option) any later version.
14 ;;; GNU Guix is distributed in the hope that it will be useful, but
15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 ;;; GNU General Public License for more details.
19 ;;; You should have received a copy of the GNU General Public License
20 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
22 (define-module (gnu packages bioconductor)
23 #:use-module ((guix licenses) #:prefix license:)
24 #:use-module (guix packages)
25 #:use-module (guix download)
26 #:use-module (guix git-download)
27 #:use-module (guix build-system r)
28 #:use-module (gnu packages)
29 #:use-module (gnu packages base)
30 #:use-module (gnu packages bioinformatics)
31 #:use-module (gnu packages cran)
32 #:use-module (gnu packages compression)
33 #:use-module (gnu packages gcc)
34 #:use-module (gnu packages graph)
35 #:use-module (gnu packages graphviz)
36 #:use-module (gnu packages haskell-xyz)
37 #:use-module (gnu packages image)
38 #:use-module (gnu packages maths)
39 #:use-module (gnu packages netpbm)
40 #:use-module (gnu packages perl)
41 #:use-module (gnu packages pkg-config)
42 #:use-module (gnu packages statistics)
43 #:use-module (gnu packages web)
44 #:use-module (gnu packages xml)
45 #:use-module (srfi srfi-1))
50 (define-public r-reactome-db
52 (name "r-reactome-db")
57 (uri (bioconductor-uri "reactome.db" version 'annotation))
60 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
61 (properties `((upstream-name . "reactome.db")))
62 (build-system r-build-system)
64 `(("r-annotationdbi" ,r-annotationdbi)))
65 (home-page "https://bioconductor.org/packages/reactome.db/")
66 (synopsis "Annotation maps for reactome")
68 "This package provides a set of annotation maps for the REACTOME
69 database, assembled using data from REACTOME.")
70 (license license:cc-by4.0)))
72 (define-public r-bsgenome-celegans-ucsc-ce6
74 (name "r-bsgenome-celegans-ucsc-ce6")
78 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
82 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
84 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
85 (build-system r-build-system)
87 `(("r-bsgenome" ,r-bsgenome)))
89 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
90 (synopsis "Full genome sequences for Worm")
92 "This package provides full genome sequences for Caenorhabditis
93 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
95 (license license:artistic2.0)))
97 (define-public r-bsgenome-celegans-ucsc-ce10
99 (name "r-bsgenome-celegans-ucsc-ce10")
103 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
104 version 'annotation))
107 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
109 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
110 (build-system r-build-system)
112 `(("r-bsgenome" ,r-bsgenome)))
114 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
115 (synopsis "Full genome sequences for Worm")
117 "This package provides full genome sequences for Caenorhabditis
118 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
120 (license license:artistic2.0)))
122 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
124 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
128 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
129 version 'annotation))
132 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
134 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
135 (build-system r-build-system)
137 `(("r-bsgenome" ,r-bsgenome)))
139 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
140 (synopsis "Full genome sequences for Fly")
142 "This package provides full genome sequences for Drosophila
143 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
145 (license license:artistic2.0)))
147 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
149 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
153 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
154 version 'annotation))
157 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
159 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
160 (build-system r-build-system)
162 `(("r-bsgenome" ,r-bsgenome)))
164 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
165 (synopsis "Full genome sequences for Fly")
167 "This package provides full genome sequences for Drosophila
168 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
169 Biostrings objects.")
170 (license license:artistic2.0)))
172 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
174 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
178 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
179 version 'annotation))
182 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
184 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
185 (build-system r-build-system)
187 `(("r-bsgenome" ,r-bsgenome)
188 ("r-bsgenome-dmelanogaster-ucsc-dm3"
189 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
190 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
191 (synopsis "Full masked genome sequences for Fly")
193 "This package provides full masked genome sequences for Drosophila
194 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
195 Biostrings objects. The sequences are the same as in
196 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
197 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
198 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
199 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
200 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
201 (license license:artistic2.0)))
203 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
205 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
209 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
210 version 'annotation))
213 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
215 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
216 (build-system r-build-system)
218 `(("r-bsgenome" ,r-bsgenome)))
220 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
221 (synopsis "Full genome sequences for Homo sapiens")
223 "This package provides full genome sequences for Homo sapiens from
224 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
225 (license license:artistic2.0)))
227 (define-public r-bsgenome-hsapiens-ncbi-grch38
229 (name "r-bsgenome-hsapiens-ncbi-grch38")
234 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
235 version 'annotation))
238 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
239 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
240 (build-system r-build-system)
241 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
243 "https://bioconductor.org/packages/release/data/annotation/html/\
244 BSgenome.Hsapiens.NCBI.GRCh38.html")
245 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
247 "This package provides full genome sequences for Homo sapiens (Human) as
248 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
249 (license license:artistic2.0)))
251 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
253 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
257 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
258 version 'annotation))
261 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
263 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
264 (build-system r-build-system)
266 `(("r-bsgenome" ,r-bsgenome)
267 ("r-bsgenome-hsapiens-ucsc-hg19"
268 ,r-bsgenome-hsapiens-ucsc-hg19)))
269 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
270 (synopsis "Full masked genome sequences for Homo sapiens")
272 "This package provides full genome sequences for Homo sapiens (Human) as
273 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
274 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
275 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
276 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
277 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
278 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
280 (license license:artistic2.0)))
282 (define-public r-bsgenome-mmusculus-ucsc-mm9
284 (name "r-bsgenome-mmusculus-ucsc-mm9")
288 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
289 version 'annotation))
292 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
294 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
295 (build-system r-build-system)
297 `(("r-bsgenome" ,r-bsgenome)))
299 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
300 (synopsis "Full genome sequences for Mouse")
302 "This package provides full genome sequences for Mus musculus (Mouse) as
303 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
304 (license license:artistic2.0)))
306 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
308 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
312 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
313 version 'annotation))
316 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
318 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
319 (build-system r-build-system)
321 `(("r-bsgenome" ,r-bsgenome)
322 ("r-bsgenome-mmusculus-ucsc-mm9"
323 ,r-bsgenome-mmusculus-ucsc-mm9)))
324 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
325 (synopsis "Full masked genome sequences for Mouse")
327 "This package provides full genome sequences for Mus musculus (Mouse) as
328 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
329 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
330 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
331 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
332 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
333 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
335 (license license:artistic2.0)))
337 (define-public r-bsgenome-mmusculus-ucsc-mm10
339 (name "r-bsgenome-mmusculus-ucsc-mm10")
343 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
344 version 'annotation))
347 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
349 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
350 (build-system r-build-system)
352 `(("r-bsgenome" ,r-bsgenome)))
354 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
355 (synopsis "Full genome sequences for Mouse")
357 "This package provides full genome sequences for Mus
358 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
359 in Biostrings objects.")
360 (license license:artistic2.0)))
362 (define-public r-org-ce-eg-db
364 (name "r-org-ce-eg-db")
368 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
371 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
373 `((upstream-name . "org.Ce.eg.db")))
374 (build-system r-build-system)
376 `(("r-annotationdbi" ,r-annotationdbi)))
377 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
378 (synopsis "Genome wide annotation for Worm")
380 "This package provides mappings from Entrez gene identifiers to various
381 annotations for the genome of the model worm Caenorhabditis elegans.")
382 (license license:artistic2.0)))
384 (define-public r-org-dm-eg-db
386 (name "r-org-dm-eg-db")
390 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
393 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
395 `((upstream-name . "org.Dm.eg.db")))
396 (build-system r-build-system)
398 `(("r-annotationdbi" ,r-annotationdbi)))
399 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
400 (synopsis "Genome wide annotation for Fly")
402 "This package provides mappings from Entrez gene identifiers to various
403 annotations for the genome of the model fruit fly Drosophila melanogaster.")
404 (license license:artistic2.0)))
406 (define-public r-org-dr-eg-db
408 (name "r-org-dr-eg-db")
412 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
415 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
417 `((upstream-name . "org.Dr.eg.db")))
418 (build-system r-build-system)
420 `(("r-annotationdbi" ,r-annotationdbi)))
421 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
422 (synopsis "Annotation for Zebrafish")
424 "This package provides genome wide annotations for Zebrafish, primarily
425 based on mapping using Entrez Gene identifiers.")
426 (license license:artistic2.0)))
428 (define-public r-org-hs-eg-db
430 (name "r-org-hs-eg-db")
434 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
437 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
439 `((upstream-name . "org.Hs.eg.db")))
440 (build-system r-build-system)
442 `(("r-annotationdbi" ,r-annotationdbi)))
443 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
444 (synopsis "Genome wide annotation for Human")
446 "This package contains genome-wide annotations for Human, primarily based
447 on mapping using Entrez Gene identifiers.")
448 (license license:artistic2.0)))
450 (define-public r-org-mm-eg-db
452 (name "r-org-mm-eg-db")
456 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
459 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
461 `((upstream-name . "org.Mm.eg.db")))
462 (build-system r-build-system)
464 `(("r-annotationdbi" ,r-annotationdbi)))
465 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
466 (synopsis "Genome wide annotation for Mouse")
468 "This package provides mappings from Entrez gene identifiers to various
469 annotations for the genome of the model mouse Mus musculus.")
470 (license license:artistic2.0)))
472 (define-public r-bsgenome-hsapiens-ucsc-hg19
474 (name "r-bsgenome-hsapiens-ucsc-hg19")
478 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
479 version 'annotation))
482 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
484 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
485 (build-system r-build-system)
487 `(("r-bsgenome" ,r-bsgenome)))
489 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
490 (synopsis "Full genome sequences for Homo sapiens")
492 "This package provides full genome sequences for Homo sapiens as provided
493 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
494 (license license:artistic2.0)))
496 (define-public r-bsgenome-hsapiens-ucsc-hg38
498 (name "r-bsgenome-hsapiens-ucsc-hg38")
502 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
503 version 'annotation))
506 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
508 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
509 (build-system r-build-system)
511 `(("r-bsgenome" ,r-bsgenome)))
513 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
514 (synopsis "Full genome sequences for Homo sapiens")
516 "This package provides full genome sequences for Homo sapiens (Human)
517 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
518 (license license:artistic2.0)))
520 (define-public r-ensdb-hsapiens-v75
522 (name "r-ensdb-hsapiens-v75")
527 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
530 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
532 `((upstream-name . "EnsDb.Hsapiens.v75")))
533 (build-system r-build-system)
535 `(("r-ensembldb" ,r-ensembldb)))
536 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
537 (synopsis "Ensembl based annotation package")
539 "This package exposes an annotation database generated from Ensembl.")
540 (license license:artistic2.0)))
542 (define-public r-genelendatabase
544 (name "r-genelendatabase")
549 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
552 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
554 `((upstream-name . "geneLenDataBase")))
555 (build-system r-build-system)
557 `(("r-rtracklayer" ,r-rtracklayer)
558 ("r-genomicfeatures" ,r-genomicfeatures)))
559 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
560 (synopsis "Lengths of mRNA transcripts for a number of genomes")
562 "This package provides the lengths of mRNA transcripts for a number of
563 genomes and gene ID formats, largely based on the UCSC table browser.")
564 (license license:lgpl2.0+)))
566 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
568 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
572 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
573 version 'annotation))
576 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
578 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
579 (build-system r-build-system)
581 `(("r-genomicfeatures" ,r-genomicfeatures)))
583 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
584 (synopsis "Annotation package for human genome in TxDb format")
586 "This package provides an annotation database of Homo sapiens genome
587 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
588 track. The database is exposed as a @code{TxDb} object.")
589 (license license:artistic2.0)))
591 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
593 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
597 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
598 version 'annotation))
601 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
603 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
604 (build-system r-build-system)
606 `(("r-genomicfeatures" ,r-genomicfeatures)))
608 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
609 (synopsis "Annotation package for human genome in TxDb format")
611 "This package provides an annotation database of Homo sapiens genome
612 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
613 track. The database is exposed as a @code{TxDb} object.")
614 (license license:artistic2.0)))
616 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
618 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
622 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
623 version 'annotation))
626 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
628 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
629 (build-system r-build-system)
631 `(("r-genomicfeatures" ,r-genomicfeatures)
632 ("r-annotationdbi" ,r-annotationdbi)))
634 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
635 (synopsis "Annotation package for mouse genome in TxDb format")
637 "This package provides an annotation database of Mouse genome data. It
638 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
639 database is exposed as a @code{TxDb} object.")
640 (license license:artistic2.0)))
642 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
644 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
648 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
649 version 'annotation))
652 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
654 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
655 (build-system r-build-system)
657 `(("r-bsgenome" ,r-bsgenome)
658 ("r-genomicfeatures" ,r-genomicfeatures)
659 ("r-annotationdbi" ,r-annotationdbi)))
661 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
662 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
664 "This package loads a TxDb object, which is an R interface to
665 prefabricated databases contained in this package. This package provides
666 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
667 based on the knownGene track.")
668 (license license:artistic2.0)))
670 (define-public r-txdb-celegans-ucsc-ce6-ensgene
672 (name "r-txdb-celegans-ucsc-ce6-ensgene")
677 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
678 version 'annotation))
681 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
683 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
684 (build-system r-build-system)
686 `(("r-annotationdbi" ,r-annotationdbi)
687 ("r-genomicfeatures" ,r-genomicfeatures)))
688 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
689 (synopsis "Annotation package for C elegans TxDb objects")
691 "This package exposes a C elegans annotation database generated from UCSC
692 by exposing these as TxDb objects.")
693 (license license:artistic2.0)))
695 (define-public r-fdb-infiniummethylation-hg19
697 (name "r-fdb-infiniummethylation-hg19")
701 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
702 version 'annotation))
705 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
707 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
708 (build-system r-build-system)
710 `(("r-biostrings" ,r-biostrings)
711 ("r-genomicfeatures" ,r-genomicfeatures)
712 ("r-annotationdbi" ,r-annotationdbi)
713 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
714 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
715 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
716 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
718 "This is an annotation package for Illumina Infinium DNA methylation
719 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
721 (license license:artistic2.0)))
723 (define-public r-illuminahumanmethylationepicmanifest
725 (name "r-illuminahumanmethylationepicmanifest")
729 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
730 version 'annotation))
733 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
735 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
736 (build-system r-build-system)
738 `(("r-minfi" ,r-minfi)))
739 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
740 (synopsis "Manifest for Illumina's EPIC methylation arrays")
742 "This is a manifest package for Illumina's EPIC methylation arrays.")
743 (license license:artistic2.0)))
745 (define-public r-ideoviz
751 (uri (bioconductor-uri "IdeoViz" version))
754 "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50"))))
755 (build-system r-build-system)
757 `(("r-biobase" ,r-biobase)
758 ("r-iranges" ,r-iranges)
759 ("r-genomicranges" ,r-genomicranges)
760 ("r-rcolorbrewer" ,r-rcolorbrewer)
761 ("r-rtracklayer" ,r-rtracklayer)
762 ("r-genomeinfodb" ,r-genomeinfodb)))
763 (home-page "https://bioconductor.org/packages/IdeoViz/")
764 (synopsis "Plots data along a chromosomal ideogram")
765 (description "This package provides functions to plot data associated with
766 arbitrary genomic intervals along chromosomal ideogram.")
767 (license license:gpl2)))
769 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
770 ;; from Bioconductor.
771 (define-public r-deconstructsigs
773 (name "r-deconstructsigs")
777 (uri (cran-uri "deconstructSigs" version))
780 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
782 `((upstream-name . "deconstructSigs")))
783 (build-system r-build-system)
785 `(("r-bsgenome" ,r-bsgenome)
786 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
787 ("r-genomeinfodb" ,r-genomeinfodb)
788 ("r-reshape2" ,r-reshape2)))
789 (home-page "https://github.com/raerose01/deconstructSigs")
790 (synopsis "Identifies signatures present in a tumor sample")
791 (description "This package takes sample information in the form of the
792 fraction of mutations in each of 96 trinucleotide contexts and identifies
793 the weighted combination of published signatures that, when summed, most
794 closely reconstructs the mutational profile.")
795 (license license:gpl2+)))
797 ;; This is a CRAN package, but it depends on Bioconductor packages.
805 (uri (cran-uri "NMF" version))
808 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
809 (properties `((upstream-name . "NMF")))
810 (build-system r-build-system)
812 `(("r-cluster" ,r-cluster)
813 ("r-biobase" ,r-biobase)
814 ("r-biocmanager" ,r-biocmanager)
815 ("r-bigmemory" ,r-bigmemory) ; suggested
816 ("r-synchronicity" ,r-synchronicity) ; suggested
817 ("r-colorspace" ,r-colorspace)
818 ("r-digest" ,r-digest)
819 ("r-doparallel" ,r-doparallel)
820 ("r-foreach" ,r-foreach)
821 ("r-ggplot2" ,r-ggplot2)
822 ("r-gridbase" ,r-gridbase)
823 ("r-pkgmaker" ,r-pkgmaker)
824 ("r-rcolorbrewer" ,r-rcolorbrewer)
825 ("r-registry" ,r-registry)
826 ("r-reshape2" ,r-reshape2)
827 ("r-rngtools" ,r-rngtools)
828 ("r-stringr" ,r-stringr)))
830 `(("r-knitr" ,r-knitr)))
831 (home-page "http://renozao.github.io/NMF")
832 (synopsis "Algorithms and framework for nonnegative matrix factorization")
834 "This package provides a framework to perform Non-negative Matrix
835 Factorization (NMF). The package implements a set of already published
836 algorithms and seeding methods, and provides a framework to test, develop and
837 plug new or custom algorithms. Most of the built-in algorithms have been
838 optimized in C++, and the main interface function provides an easy way of
839 performing parallel computations on multicore machines.")
840 (license license:gpl2+)))
842 (define-public r-do-db
848 (uri (bioconductor-uri "DO.db" version 'annotation))
851 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
853 `((upstream-name . "DO.db")))
854 (build-system r-build-system)
856 `(("r-annotationdbi" ,r-annotationdbi)))
857 (home-page "https://www.bioconductor.org/packages/DO.db/")
858 (synopsis "Annotation maps describing the entire Disease Ontology")
860 "This package provides a set of annotation maps describing the entire
862 (license license:artistic2.0)))
864 (define-public r-pasilla
871 "http://bioconductor.org/packages/release/data/experiment"
872 "/src/contrib/pasilla_" version ".tar.gz"))
875 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
876 (build-system r-build-system)
878 `(("r-biocstyle" ,r-biocstyle)
879 ("r-dexseq" ,r-dexseq)
881 ("r-rmarkdown" ,r-rmarkdown)))
882 (home-page "https://www.bioconductor.org/packages/pasilla/")
883 (synopsis "Data package with per-exon and per-gene read counts")
884 (description "This package provides per-exon and per-gene read counts
885 computed for selected genes from RNA-seq data that were presented in the
886 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
887 by Brooks et al., Genome Research 2011.")
888 (license license:lgpl2.1+)))
890 (define-public r-pfam-db
897 (uri (bioconductor-uri "PFAM.db" version 'annotation))
900 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
901 (properties `((upstream-name . "PFAM.db")))
902 (build-system r-build-system)
904 `(("r-annotationdbi" ,r-annotationdbi)))
905 (home-page "https://bioconductor.org/packages/PFAM.db")
906 (synopsis "Set of protein ID mappings for PFAM")
908 "This package provides a set of protein ID mappings for PFAM, assembled
909 using data from public repositories.")
910 (license license:artistic2.0)))
912 (define-public r-phastcons100way-ucsc-hg19
914 (name "r-phastcons100way-ucsc-hg19")
919 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
920 version 'annotation))
923 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
925 `((upstream-name . "phastCons100way.UCSC.hg19")))
926 (build-system r-build-system)
928 `(("r-bsgenome" ,r-bsgenome)
929 ("r-genomeinfodb" ,r-genomeinfodb)
930 ("r-genomicranges" ,r-genomicranges)
931 ("r-genomicscores" ,r-genomicscores)
932 ("r-iranges" ,r-iranges)
933 ("r-s4vectors" ,r-s4vectors)))
934 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
935 (synopsis "UCSC phastCons conservation scores for hg19")
937 "This package provides UCSC phastCons conservation scores for the human
938 genome (hg19) calculated from multiple alignments with other 99 vertebrate
940 (license license:artistic2.0)))
945 (define-public r-abadata
951 (uri (bioconductor-uri "ABAData" version 'experiment))
954 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
956 `((upstream-name . "ABAData")))
957 (build-system r-build-system)
959 `(("r-annotationdbi" ,r-annotationdbi)))
960 (home-page "https://www.bioconductor.org/packages/ABAData/")
961 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
963 "This package provides the data for the gene expression enrichment
964 analysis conducted in the package ABAEnrichment. The package includes three
965 datasets which are derived from the Allen Brain Atlas:
968 @item Gene expression data from Human Brain (adults) averaged across donors,
969 @item Gene expression data from the Developing Human Brain pooled into five
970 age categories and averaged across donors, and
971 @item a developmental effect score based on the Developing Human Brain
975 All datasets are restricted to protein coding genes.")
976 (license license:gpl2+)))
978 (define-public r-arrmdata
984 (uri (bioconductor-uri "ARRmData" version 'experiment))
987 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
989 `((upstream-name . "ARRmData")))
990 (build-system r-build-system)
991 (home-page "https://www.bioconductor.org/packages/ARRmData/")
992 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
994 "This package provides raw beta values from 36 samples across 3 groups
995 from Illumina 450k methylation arrays.")
996 (license license:artistic2.0)))
998 (define-public r-hsmmsinglecell
1000 (name "r-hsmmsinglecell")
1004 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1007 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1009 `((upstream-name . "HSMMSingleCell")))
1010 (build-system r-build-system)
1011 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1012 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1014 "Skeletal myoblasts undergo a well-characterized sequence of
1015 morphological and transcriptional changes during differentiation. In this
1016 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1017 under high mitogen conditions (GM) and then differentiated by switching to
1018 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1019 hundred cells taken over a time-course of serum-induced differentiation.
1020 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1021 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1022 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1023 which were then sequenced to a depth of ~4 million reads per library,
1024 resulting in a complete gene expression profile for each cell.")
1025 (license license:artistic2.0)))
1027 (define-public r-all
1033 (uri (bioconductor-uri "ALL" version 'experiment))
1036 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1037 (properties `((upstream-name . "ALL")))
1038 (build-system r-build-system)
1040 `(("r-biobase" ,r-biobase)))
1041 (home-page "https://bioconductor.org/packages/ALL")
1042 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1044 "The data consist of microarrays from 128 different individuals with
1045 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1046 are available. The data have been normalized (using rma) and it is the
1047 jointly normalized data that are available here. The data are presented in
1048 the form of an @code{exprSet} object.")
1049 (license license:artistic2.0)))
1051 (define-public r-affydata
1058 (uri (bioconductor-uri "affydata" version 'experiment))
1061 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1062 (properties `((upstream-name . "affydata")))
1063 (build-system r-build-system)
1065 `(("r-affy" ,r-affy)))
1066 (home-page "https://bioconductor.org/packages/affydata/")
1067 (synopsis "Affymetrix data for demonstration purposes")
1069 "This package provides example datasets that represent 'real world
1070 examples' of Affymetrix data, unlike the artificial examples included in the
1071 package @code{affy}.")
1072 (license license:gpl2+)))
1074 (define-public r-coverageview
1076 (name "r-coverageview")
1080 (uri (bioconductor-uri "CoverageView" version))
1083 "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj"))))
1084 (build-system r-build-system)
1086 `(("r-s4vectors" ,r-s4vectors)
1087 ("r-iranges" ,r-iranges)
1088 ("r-genomicranges" ,r-genomicranges)
1089 ("r-genomicalignments" ,r-genomicalignments)
1090 ("r-rtracklayer" ,r-rtracklayer)
1091 ("r-rsamtools" ,r-rsamtools)))
1092 (home-page "https://bioconductor.org/packages/CoverageView/")
1093 (synopsis "Coverage visualization package for R")
1094 (description "This package provides a framework for the visualization of
1095 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1096 be also used for genome-wide nucleosome positioning experiments or other
1097 experiment types where it is important to have a framework in order to inspect
1098 how the coverage distributed across the genome.")
1099 (license license:artistic2.0)))
1101 (define-public r-cummerbund
1103 (name "r-cummerbund")
1107 (uri (bioconductor-uri "cummeRbund" version))
1110 "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc"))))
1111 (build-system r-build-system)
1113 `(("r-biobase" ,r-biobase)
1114 ("r-biocgenerics" ,r-biocgenerics)
1115 ("r-fastcluster", r-fastcluster)
1116 ("r-ggplot2" ,r-ggplot2)
1119 ("r-reshape2" ,r-reshape2)
1120 ("r-rsqlite" ,r-rsqlite)
1121 ("r-rtracklayer" ,r-rtracklayer)
1122 ("r-s4vectors" ,r-s4vectors)))
1123 (home-page "https://bioconductor.org/packages/cummeRbund/")
1124 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1125 (description "This package allows for persistent storage, access,
1126 exploration, and manipulation of Cufflinks high-throughput sequencing
1127 data. In addition, provides numerous plotting functions for commonly
1128 used visualizations.")
1129 (license license:artistic2.0)))
1131 (define-public r-curatedtcgadata
1133 (name "r-curatedtcgadata")
1138 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1141 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1143 `((upstream-name . "curatedTCGAData")))
1144 (build-system r-build-system)
1146 `(("r-annotationhub" ,r-annotationhub)
1147 ("r-experimenthub" ,r-experimenthub)
1148 ("r-hdf5array" ,r-hdf5array)
1149 ("r-multiassayexperiment" ,r-multiassayexperiment)
1150 ("r-s4vectors" ,r-s4vectors)
1151 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1152 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1153 (synopsis "Curated data from The Cancer Genome Atlas")
1155 "This package provides publicly available data from The Cancer Genome
1156 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1157 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1158 number, mutation, microRNA, protein, and others) with clinical / pathological
1159 data. It also links assay barcodes with patient identifiers, enabling
1160 harmonized subsetting of rows (features) and columns (patients / samples)
1161 across the entire multi-'omics experiment.")
1162 (license license:artistic2.0)))
1167 (define-public r-biocversion
1169 (name "r-biocversion")
1174 (uri (bioconductor-uri "BiocVersion" version))
1177 "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz"))))
1178 (properties `((upstream-name . "BiocVersion")))
1179 (build-system r-build-system)
1180 (home-page "https://bioconductor.org/packages/BiocVersion/")
1181 (synopsis "Set the appropriate version of Bioconductor packages")
1183 "This package provides repository information for the appropriate version
1185 (license license:artistic2.0)))
1187 (define-public r-biocgenerics
1189 (name "r-biocgenerics")
1193 (uri (bioconductor-uri "BiocGenerics" version))
1196 "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk"))))
1198 `((upstream-name . "BiocGenerics")))
1199 (build-system r-build-system)
1200 (home-page "https://bioconductor.org/packages/BiocGenerics")
1201 (synopsis "S4 generic functions for Bioconductor")
1203 "This package provides S4 generic functions needed by many Bioconductor
1205 (license license:artistic2.0)))
1207 (define-public r-affycomp
1214 (uri (bioconductor-uri "affycomp" version))
1217 "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0"))))
1218 (properties `((upstream-name . "affycomp")))
1219 (build-system r-build-system)
1220 (propagated-inputs `(("r-biobase" ,r-biobase)))
1221 (home-page "https://bioconductor.org/packages/affycomp/")
1222 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1224 "The package contains functions that can be used to compare expression
1225 measures for Affymetrix Oligonucleotide Arrays.")
1226 (license license:gpl2+)))
1228 (define-public r-affycompatible
1230 (name "r-affycompatible")
1235 (uri (bioconductor-uri "AffyCompatible" version))
1238 "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd"))))
1240 `((upstream-name . "AffyCompatible")))
1241 (build-system r-build-system)
1243 `(("r-biostrings" ,r-biostrings)
1244 ("r-rcurl" ,r-rcurl)
1246 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1247 (synopsis "Work with Affymetrix GeneChip files")
1249 "This package provides an interface to Affymetrix chip annotation and
1250 sample attribute files. The package allows an easy way for users to download
1251 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1252 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1253 Command Console} (AGCC)-compatible sample annotation files.")
1254 (license license:artistic2.0)))
1256 (define-public r-affycontam
1258 (name "r-affycontam")
1263 (uri (bioconductor-uri "affyContam" version))
1266 "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i"))))
1267 (properties `((upstream-name . "affyContam")))
1268 (build-system r-build-system)
1270 `(("r-affy" ,r-affy)
1271 ("r-affydata" ,r-affydata)
1272 ("r-biobase" ,r-biobase)))
1273 (home-page "https://bioconductor.org/packages/affyContam/")
1274 (synopsis "Structured corruption of Affymetrix CEL file data")
1276 "Microarray quality assessment is a major concern of microarray analysts.
1277 This package provides some simple approaches to in silico creation of quality
1278 problems in CEL-level data to help evaluate performance of quality metrics.")
1279 (license license:artistic2.0)))
1281 (define-public r-affycoretools
1283 (name "r-affycoretools")
1288 (uri (bioconductor-uri "affycoretools" version))
1291 "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s"))))
1292 (properties `((upstream-name . "affycoretools")))
1293 (build-system r-build-system)
1295 `(("r-affy" ,r-affy)
1296 ("r-annotationdbi" ,r-annotationdbi)
1297 ("r-biobase" ,r-biobase)
1298 ("r-biocgenerics" ,r-biocgenerics)
1300 ("r-edger" ,r-edger)
1301 ("r-gcrma" ,r-gcrma)
1302 ("r-glimma" ,r-glimma)
1303 ("r-ggplot2" ,r-ggplot2)
1304 ("r-gostats" ,r-gostats)
1305 ("r-gplots" ,r-gplots)
1306 ("r-hwriter" ,r-hwriter)
1307 ("r-lattice" ,r-lattice)
1308 ("r-limma" ,r-limma)
1309 ("r-oligoclasses" ,r-oligoclasses)
1310 ("r-reportingtools" ,r-reportingtools)
1311 ("r-rsqlite" ,r-rsqlite)
1312 ("r-s4vectors" ,r-s4vectors)
1313 ("r-xtable" ,r-xtable)))
1315 `(("r-knitr" ,r-knitr)))
1316 (home-page "https://bioconductor.org/packages/affycoretools/")
1317 (synopsis "Functions for analyses with Affymetrix GeneChips")
1319 "This package provides various wrapper functions that have been written
1320 to streamline the more common analyses that a Biostatistician might see.")
1321 (license license:artistic2.0)))
1323 (define-public r-affxparser
1325 (name "r-affxparser")
1330 (uri (bioconductor-uri "affxparser" version))
1333 "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq"))))
1334 (properties `((upstream-name . "affxparser")))
1335 (build-system r-build-system)
1336 (home-page "https://github.com/HenrikBengtsson/affxparser")
1337 (synopsis "Affymetrix File Parsing SDK")
1339 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1340 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1341 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1342 are supported. Currently, there are methods for reading @dfn{chip definition
1343 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1344 either in full or in part. For example, probe signals from a few probesets
1345 can be extracted very quickly from a set of CEL files into a convenient list
1347 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1349 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1351 (define-public r-annotate
1358 (uri (bioconductor-uri "annotate" version))
1361 "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w"))))
1362 (build-system r-build-system)
1364 `(("r-annotationdbi" ,r-annotationdbi)
1365 ("r-biobase" ,r-biobase)
1366 ("r-biocgenerics" ,r-biocgenerics)
1368 ("r-rcurl" ,r-rcurl)
1370 ("r-xtable" ,r-xtable)))
1372 "https://bioconductor.org/packages/annotate")
1373 (synopsis "Annotation for microarrays")
1374 (description "This package provides R environments for the annotation of
1376 (license license:artistic2.0)))
1378 (define-public r-hpar
1385 (uri (bioconductor-uri "hpar" version))
1388 "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9"))))
1389 (build-system r-build-system)
1391 `(("r-knitr" ,r-knitr)))
1392 (home-page "https://bioconductor.org/packages/hpar/")
1393 (synopsis "Human Protein Atlas in R")
1394 (description "This package provides a simple interface to and data from
1395 the Human Protein Atlas project.")
1396 (license license:artistic2.0)))
1398 (define-public r-regioner
1405 (uri (bioconductor-uri "regioneR" version))
1408 "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c"))))
1409 (properties `((upstream-name . "regioneR")))
1410 (build-system r-build-system)
1412 `(("r-biostrings" ,r-biostrings)
1413 ("r-bsgenome" ,r-bsgenome)
1414 ("r-genomeinfodb" ,r-genomeinfodb)
1415 ("r-genomicranges" ,r-genomicranges)
1416 ("r-iranges" ,r-iranges)
1417 ("r-memoise" ,r-memoise)
1418 ("r-rtracklayer" ,r-rtracklayer)
1419 ("r-s4vectors" ,r-s4vectors)))
1421 `(("r-knitr" ,r-knitr)))
1422 (home-page "https://bioconductor.org/packages/regioneR/")
1423 (synopsis "Association analysis of genomic regions")
1424 (description "This package offers a statistical framework based on
1425 customizable permutation tests to assess the association between genomic
1426 region sets and other genomic features.")
1427 (license license:artistic2.0)))
1429 (define-public r-reportingtools
1431 (name "r-reportingtools")
1436 (uri (bioconductor-uri "ReportingTools" version))
1439 "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx"))))
1441 `((upstream-name . "ReportingTools")))
1442 (build-system r-build-system)
1444 `(("r-annotate" ,r-annotate)
1445 ("r-annotationdbi" ,r-annotationdbi)
1446 ("r-biobase" ,r-biobase)
1447 ("r-biocgenerics" ,r-biocgenerics)
1448 ("r-category" ,r-category)
1449 ("r-deseq2" ,r-deseq2)
1450 ("r-edger" ,r-edger)
1451 ("r-ggbio" ,r-ggbio)
1452 ("r-ggplot2" ,r-ggplot2)
1453 ("r-gostats" ,r-gostats)
1454 ("r-gseabase" ,r-gseabase)
1455 ("r-hwriter" ,r-hwriter)
1456 ("r-iranges" ,r-iranges)
1457 ("r-knitr" ,r-knitr)
1458 ("r-lattice" ,r-lattice)
1459 ("r-limma" ,r-limma)
1460 ("r-pfam-db" ,r-pfam-db)
1461 ("r-r-utils" ,r-r-utils)
1464 `(("r-knitr" ,r-knitr)))
1465 (home-page "https://bioconductor.org/packages/ReportingTools/")
1466 (synopsis "Tools for making reports in various formats")
1468 "The ReportingTools package enables users to easily display reports of
1469 analysis results generated from sources such as microarray and sequencing
1470 data. The package allows users to create HTML pages that may be viewed on a
1471 web browser, or in other formats. Users can generate tables with sortable and
1472 filterable columns, make and display plots, and link table entries to other
1473 data sources such as NCBI or larger plots within the HTML page. Using the
1474 package, users can also produce a table of contents page to link various
1475 reports together for a particular project that can be viewed in a web
1477 (license license:artistic2.0)))
1479 (define-public r-geneplotter
1481 (name "r-geneplotter")
1486 (uri (bioconductor-uri "geneplotter" version))
1489 "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5"))))
1490 (build-system r-build-system)
1492 `(("r-annotate" ,r-annotate)
1493 ("r-annotationdbi" ,r-annotationdbi)
1494 ("r-biobase" ,r-biobase)
1495 ("r-biocgenerics" ,r-biocgenerics)
1496 ("r-lattice" ,r-lattice)
1497 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1498 (home-page "https://bioconductor.org/packages/geneplotter")
1499 (synopsis "Graphics functions for genomic data")
1501 "This package provides functions for plotting genomic data.")
1502 (license license:artistic2.0)))
1504 (define-public r-oligoclasses
1506 (name "r-oligoclasses")
1511 (uri (bioconductor-uri "oligoClasses" version))
1514 "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67"))))
1515 (properties `((upstream-name . "oligoClasses")))
1516 (build-system r-build-system)
1518 `(("r-affyio" ,r-affyio)
1519 ("r-biobase" ,r-biobase)
1520 ("r-biocgenerics" ,r-biocgenerics)
1521 ("r-biocmanager" ,r-biocmanager)
1522 ("r-biostrings" ,r-biostrings)
1525 ("r-foreach" ,r-foreach)
1526 ("r-genomicranges" ,r-genomicranges)
1527 ("r-iranges" ,r-iranges)
1528 ("r-rsqlite" ,r-rsqlite)
1529 ("r-s4vectors" ,r-s4vectors)
1530 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1531 (home-page "https://bioconductor.org/packages/oligoClasses/")
1532 (synopsis "Classes for high-throughput arrays")
1534 "This package contains class definitions, validity checks, and
1535 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1537 (license license:gpl2+)))
1539 (define-public r-oligo
1546 (uri (bioconductor-uri "oligo" version))
1549 "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd"))))
1550 (properties `((upstream-name . "oligo")))
1551 (build-system r-build-system)
1552 (inputs `(("zlib" ,zlib)))
1554 `(("r-affxparser" ,r-affxparser)
1555 ("r-affyio" ,r-affyio)
1556 ("r-biobase" ,r-biobase)
1557 ("r-biocgenerics" ,r-biocgenerics)
1558 ("r-biostrings" ,r-biostrings)
1561 ("r-oligoclasses" ,r-oligoclasses)
1562 ("r-preprocesscore" ,r-preprocesscore)
1563 ("r-rsqlite" ,r-rsqlite)
1564 ("r-zlibbioc" ,r-zlibbioc)))
1566 `(("r-knitr" ,r-knitr)))
1567 (home-page "https://bioconductor.org/packages/oligo/")
1568 (synopsis "Preprocessing tools for oligonucleotide arrays")
1570 "This package provides a package to analyze oligonucleotide
1571 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1572 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1573 (license license:lgpl2.0+)))
1575 (define-public r-qvalue
1582 (uri (bioconductor-uri "qvalue" version))
1585 "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f"))))
1586 (build-system r-build-system)
1588 `(("r-ggplot2" ,r-ggplot2)
1589 ("r-reshape2" ,r-reshape2)))
1591 `(("r-knitr" ,r-knitr)))
1592 (home-page "https://github.com/StoreyLab/qvalue")
1593 (synopsis "Q-value estimation for false discovery rate control")
1595 "This package takes a list of p-values resulting from the simultaneous
1596 testing of many hypotheses and estimates their q-values and local @dfn{false
1597 discovery rate} (FDR) values. The q-value of a test measures the proportion
1598 of false positives incurred when that particular test is called significant.
1599 The local FDR measures the posterior probability the null hypothesis is true
1600 given the test's p-value. Various plots are automatically generated, allowing
1601 one to make sensible significance cut-offs. The software can be applied to
1602 problems in genomics, brain imaging, astrophysics, and data mining.")
1603 ;; Any version of the LGPL.
1604 (license license:lgpl3+)))
1606 (define-public r-diffbind
1613 (uri (bioconductor-uri "DiffBind" version))
1616 "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5"))))
1617 (properties `((upstream-name . "DiffBind")))
1618 (build-system r-build-system)
1622 `(("r-amap" ,r-amap)
1623 ("r-biocparallel" ,r-biocparallel)
1624 ("r-deseq2" ,r-deseq2)
1625 ("r-dplyr" ,r-dplyr)
1626 ("r-edger" ,r-edger)
1627 ("r-genomicalignments" ,r-genomicalignments)
1628 ("r-genomicranges" ,r-genomicranges)
1629 ("r-ggplot2" ,r-ggplot2)
1630 ("r-ggrepel" ,r-ggrepel)
1631 ("r-gplots" ,r-gplots)
1632 ("r-iranges" ,r-iranges)
1633 ("r-lattice" ,r-lattice)
1634 ("r-limma" ,r-limma)
1635 ("r-locfit" ,r-locfit)
1636 ("r-rcolorbrewer" , r-rcolorbrewer)
1638 ("r-rhtslib" ,r-rhtslib)
1639 ("r-rsamtools" ,r-rsamtools)
1640 ("r-s4vectors" ,r-s4vectors)
1641 ("r-summarizedexperiment" ,r-summarizedexperiment)
1642 ("r-systempiper" ,r-systempiper)))
1643 (home-page "https://bioconductor.org/packages/DiffBind")
1644 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1646 "This package computes differentially bound sites from multiple
1647 ChIP-seq experiments using affinity (quantitative) data. Also enables
1648 occupancy (overlap) analysis and plotting functions.")
1649 (license license:artistic2.0)))
1651 (define-public r-ripseeker
1653 (name "r-ripseeker")
1658 (uri (bioconductor-uri "RIPSeeker" version))
1661 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1662 (properties `((upstream-name . "RIPSeeker")))
1663 (build-system r-build-system)
1665 `(("r-s4vectors" ,r-s4vectors)
1666 ("r-iranges" ,r-iranges)
1667 ("r-genomicranges" ,r-genomicranges)
1668 ("r-summarizedexperiment" ,r-summarizedexperiment)
1669 ("r-rsamtools" ,r-rsamtools)
1670 ("r-genomicalignments" ,r-genomicalignments)
1671 ("r-rtracklayer" ,r-rtracklayer)))
1672 (home-page "https://bioconductor.org/packages/RIPSeeker")
1674 "Identifying protein-associated transcripts from RIP-seq experiments")
1676 "This package infers and discriminates RIP peaks from RIP-seq alignments
1677 using two-state HMM with negative binomial emission probability. While
1678 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1679 a suite of bioinformatics tools integrated within this self-contained software
1680 package comprehensively addressing issues ranging from post-alignments
1681 processing to visualization and annotation.")
1682 (license license:gpl2)))
1684 (define-public r-multtest
1691 (uri (bioconductor-uri "multtest" version))
1694 "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2"))))
1695 (build-system r-build-system)
1697 `(("r-survival" ,r-survival)
1698 ("r-biocgenerics" ,r-biocgenerics)
1699 ("r-biobase" ,r-biobase)
1700 ("r-mass" ,r-mass)))
1701 (home-page "https://bioconductor.org/packages/multtest")
1702 (synopsis "Resampling-based multiple hypothesis testing")
1704 "This package can do non-parametric bootstrap and permutation
1705 resampling-based multiple testing procedures (including empirical Bayes
1706 methods) for controlling the family-wise error rate (FWER), generalized
1707 family-wise error rate (gFWER), tail probability of the proportion of
1708 false positives (TPPFP), and false discovery rate (FDR). Several choices
1709 of bootstrap-based null distribution are implemented (centered, centered
1710 and scaled, quantile-transformed). Single-step and step-wise methods are
1711 available. Tests based on a variety of T- and F-statistics (including
1712 T-statistics based on regression parameters from linear and survival models
1713 as well as those based on correlation parameters) are included. When probing
1714 hypotheses with T-statistics, users may also select a potentially faster null
1715 distribution which is multivariate normal with mean zero and variance
1716 covariance matrix derived from the vector influence function. Results are
1717 reported in terms of adjusted P-values, confidence regions and test statistic
1718 cutoffs. The procedures are directly applicable to identifying differentially
1719 expressed genes in DNA microarray experiments.")
1720 (license license:lgpl3)))
1722 (define-public r-graph
1728 (uri (bioconductor-uri "graph" version))
1731 "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g"))))
1732 (build-system r-build-system)
1734 `(("r-biocgenerics" ,r-biocgenerics)))
1735 (home-page "https://bioconductor.org/packages/graph")
1736 (synopsis "Handle graph data structures in R")
1738 "This package implements some simple graph handling capabilities for R.")
1739 (license license:artistic2.0)))
1741 ;; This is a CRAN package, but it depends on a Bioconductor package.
1742 (define-public r-ggm
1749 (uri (cran-uri "ggm" version))
1752 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1753 (properties `((upstream-name . "ggm")))
1754 (build-system r-build-system)
1756 `(("r-graph" ,r-graph)
1757 ("r-igraph" ,r-igraph)))
1758 (home-page "https://cran.r-project.org/package=ggm")
1759 (synopsis "Functions for graphical Markov models")
1761 "This package provides functions and datasets for maximum likelihood
1762 fitting of some classes of graphical Markov models.")
1763 (license license:gpl2+)))
1765 (define-public r-codedepends
1767 (name "r-codedepends")
1772 (uri (cran-uri "CodeDepends" version))
1775 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1776 (properties `((upstream-name . "CodeDepends")))
1777 (build-system r-build-system)
1779 `(("r-codetools" ,r-codetools)
1780 ("r-graph" ,r-graph)
1782 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1783 (synopsis "Analysis of R code for reproducible research and code comprehension")
1785 "This package provides tools for analyzing R expressions or blocks of
1786 code and determining the dependencies between them. It focuses on R scripts,
1787 but can be used on the bodies of functions. There are many facilities
1788 including the ability to summarize or get a high-level view of code,
1789 determining dependencies between variables, code improvement suggestions.")
1790 ;; Any version of the GPL
1791 (license (list license:gpl2+ license:gpl3+))))
1793 (define-public r-chippeakanno
1795 (name "r-chippeakanno")
1800 (uri (bioconductor-uri "ChIPpeakAnno" version))
1803 "199mlg0gwjy39afyk0ah6lzcm759bzxla4hgcajj0ay9jiibjqpa"))))
1804 (properties `((upstream-name . "ChIPpeakAnno")))
1805 (build-system r-build-system)
1807 `(("r-annotationdbi" ,r-annotationdbi)
1808 ("r-biobase" ,r-biobase)
1809 ("r-biocgenerics" ,r-biocgenerics)
1810 ("r-biocmanager" ,r-biocmanager)
1811 ("r-biomart" ,r-biomart)
1812 ("r-biostrings" ,r-biostrings)
1813 ("r-bsgenome" ,r-bsgenome)
1815 ("r-delayedarray" ,r-delayedarray)
1816 ("r-ensembldb" ,r-ensembldb)
1817 ("r-genomeinfodb" ,r-genomeinfodb)
1818 ("r-genomicalignments" ,r-genomicalignments)
1819 ("r-genomicfeatures" ,r-genomicfeatures)
1820 ("r-genomicranges" ,r-genomicranges)
1821 ("r-go-db" ,r-go-db)
1822 ("r-graph" ,r-graph)
1824 ("r-iranges" ,r-iranges)
1825 ("r-limma" ,r-limma)
1826 ("r-matrixstats" ,r-matrixstats)
1827 ("r-multtest" ,r-multtest)
1829 ("r-regioner" ,r-regioner)
1830 ("r-rsamtools" ,r-rsamtools)
1831 ("r-rtracklayer" ,r-rtracklayer)
1832 ("r-s4vectors" ,r-s4vectors)
1833 ("r-seqinr" ,r-seqinr)
1834 ("r-summarizedexperiment" ,r-summarizedexperiment)
1835 ("r-venndiagram" ,r-venndiagram)))
1837 `(("r-knitr" ,r-knitr)))
1838 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
1839 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1841 "The package includes functions to retrieve the sequences around the peak,
1842 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1843 custom features such as most conserved elements and other transcription factor
1844 binding sites supplied by users. Starting 2.0.5, new functions have been added
1845 for finding the peaks with bi-directional promoters with summary statistics
1846 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1847 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1848 enrichedGO (addGeneIDs).")
1849 (license license:gpl2+)))
1851 (define-public r-marray
1857 (uri (bioconductor-uri "marray" version))
1859 (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd"))))
1860 (build-system r-build-system)
1862 `(("r-limma" ,r-limma)))
1863 (home-page "https://bioconductor.org/packages/marray")
1864 (synopsis "Exploratory analysis for two-color spotted microarray data")
1865 (description "This package contains class definitions for two-color spotted
1866 microarray data. It also includes functions for data input, diagnostic plots,
1867 normalization and quality checking.")
1868 (license license:lgpl2.0+)))
1870 (define-public r-cghbase
1876 (uri (bioconductor-uri "CGHbase" version))
1878 (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf"))))
1879 (properties `((upstream-name . "CGHbase")))
1880 (build-system r-build-system)
1882 `(("r-biobase" ,r-biobase)
1883 ("r-marray" ,r-marray)))
1884 (home-page "https://bioconductor.org/packages/CGHbase")
1885 (synopsis "Base functions and classes for arrayCGH data analysis")
1886 (description "This package contains functions and classes that are needed by
1887 the @code{arrayCGH} packages.")
1888 (license license:gpl2+)))
1890 (define-public r-cghcall
1896 (uri (bioconductor-uri "CGHcall" version))
1898 (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg"))))
1899 (properties `((upstream-name . "CGHcall")))
1900 (build-system r-build-system)
1902 `(("r-biobase" ,r-biobase)
1903 ("r-cghbase" ,r-cghbase)
1904 ("r-impute" ,r-impute)
1905 ("r-dnacopy" ,r-dnacopy)
1906 ("r-snowfall" ,r-snowfall)))
1907 (home-page "https://bioconductor.org/packages/CGHcall")
1908 (synopsis "Base functions and classes for arrayCGH data analysis")
1909 (description "This package contains functions and classes that are needed by
1910 @code{arrayCGH} packages.")
1911 (license license:gpl2+)))
1913 (define-public r-qdnaseq
1919 (uri (bioconductor-uri "QDNAseq" version))
1921 (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86"))))
1922 (properties `((upstream-name . "QDNAseq")))
1923 (build-system r-build-system)
1925 `(("r-biobase" ,r-biobase)
1926 ("r-cghbase" ,r-cghbase)
1927 ("r-cghcall" ,r-cghcall)
1928 ("r-dnacopy" ,r-dnacopy)
1929 ("r-future" ,r-future)
1930 ("r-future-apply" ,r-future-apply)
1931 ("r-genomicranges" ,r-genomicranges)
1932 ("r-iranges" ,r-iranges)
1933 ("r-matrixstats" ,r-matrixstats)
1934 ("r-r-utils" ,r-r-utils)
1935 ("r-rsamtools" ,r-rsamtools)))
1936 (home-page "https://bioconductor.org/packages/QDNAseq")
1937 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1938 (description "The genome is divided into non-overlapping fixed-sized bins,
1939 number of sequence reads in each counted, adjusted with a simultaneous
1940 two-dimensional loess correction for sequence mappability and GC content, and
1941 filtered to remove spurious regions in the genome. Downstream steps of
1942 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1944 (license license:gpl2+)))
1946 (define-public r-bayseq
1953 (uri (bioconductor-uri "baySeq" version))
1956 "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj"))))
1957 (properties `((upstream-name . "baySeq")))
1958 (build-system r-build-system)
1960 `(("r-abind" ,r-abind)
1961 ("r-edger" ,r-edger)
1962 ("r-genomicranges" ,r-genomicranges)))
1963 (home-page "https://bioconductor.org/packages/baySeq/")
1964 (synopsis "Bayesian analysis of differential expression patterns in count data")
1966 "This package identifies differential expression in high-throughput count
1967 data, such as that derived from next-generation sequencing machines,
1968 calculating estimated posterior likelihoods of differential expression (or
1969 more complex hypotheses) via empirical Bayesian methods.")
1970 (license license:gpl3)))
1972 (define-public r-chipcomp
1979 (uri (bioconductor-uri "ChIPComp" version))
1982 "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp"))))
1983 (properties `((upstream-name . "ChIPComp")))
1984 (build-system r-build-system)
1986 `(("r-biocgenerics" ,r-biocgenerics)
1987 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1988 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1989 ("r-genomeinfodb" ,r-genomeinfodb)
1990 ("r-genomicranges" ,r-genomicranges)
1991 ("r-iranges" ,r-iranges)
1992 ("r-limma" ,r-limma)
1993 ("r-rsamtools" ,r-rsamtools)
1994 ("r-rtracklayer" ,r-rtracklayer)
1995 ("r-s4vectors" ,r-s4vectors)))
1996 (home-page "https://bioconductor.org/packages/ChIPComp")
1997 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1999 "ChIPComp implements a statistical method for quantitative comparison of
2000 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2001 sites across multiple conditions considering matching control in ChIP-seq
2003 ;; Any version of the GPL.
2004 (license license:gpl3+)))
2006 (define-public r-riboprofiling
2008 (name "r-riboprofiling")
2013 (uri (bioconductor-uri "RiboProfiling" version))
2016 "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha"))))
2017 (properties `((upstream-name . "RiboProfiling")))
2018 (build-system r-build-system)
2020 `(("r-biocgenerics" ,r-biocgenerics)
2021 ("r-biostrings" ,r-biostrings)
2022 ("r-data-table" ,r-data-table)
2023 ("r-genomeinfodb" ,r-genomeinfodb)
2024 ("r-genomicalignments" ,r-genomicalignments)
2025 ("r-genomicfeatures" ,r-genomicfeatures)
2026 ("r-genomicranges" ,r-genomicranges)
2027 ("r-ggbio" ,r-ggbio)
2028 ("r-ggplot2" ,r-ggplot2)
2029 ("r-iranges" ,r-iranges)
2031 ("r-reshape2" ,r-reshape2)
2032 ("r-rsamtools" ,r-rsamtools)
2033 ("r-rtracklayer" ,r-rtracklayer)
2034 ("r-s4vectors" ,r-s4vectors)
2035 ("r-sqldf" ,r-sqldf)))
2037 `(("r-knitr" ,r-knitr)))
2038 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2039 (synopsis "Ribosome profiling data analysis")
2040 (description "Starting with a BAM file, this package provides the
2041 necessary functions for quality assessment, read start position recalibration,
2042 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2043 of count data: pairs, log fold-change, codon frequency and coverage
2044 assessment, principal component analysis on codon coverage.")
2045 (license license:gpl3)))
2047 (define-public r-riboseqr
2054 (uri (bioconductor-uri "riboSeqR" version))
2057 "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk"))))
2058 (properties `((upstream-name . "riboSeqR")))
2059 (build-system r-build-system)
2061 `(("r-abind" ,r-abind)
2062 ("r-bayseq" ,r-bayseq)
2063 ("r-genomeinfodb" ,r-genomeinfodb)
2064 ("r-genomicranges" ,r-genomicranges)
2065 ("r-iranges" ,r-iranges)
2066 ("r-rsamtools" ,r-rsamtools)
2067 ("r-seqlogo" ,r-seqlogo)))
2068 (home-page "https://bioconductor.org/packages/riboSeqR/")
2069 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2071 "This package provides plotting functions, frameshift detection and
2072 parsing of genetic sequencing data from ribosome profiling experiments.")
2073 (license license:gpl3)))
2075 (define-public r-interactionset
2077 (name "r-interactionset")
2082 (uri (bioconductor-uri "InteractionSet" version))
2085 "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v"))))
2087 `((upstream-name . "InteractionSet")))
2088 (build-system r-build-system)
2090 `(("r-biocgenerics" ,r-biocgenerics)
2091 ("r-genomeinfodb" ,r-genomeinfodb)
2092 ("r-genomicranges" ,r-genomicranges)
2093 ("r-iranges" ,r-iranges)
2094 ("r-matrix" ,r-matrix)
2096 ("r-s4vectors" ,r-s4vectors)
2097 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2099 `(("r-knitr" ,r-knitr)))
2100 (home-page "https://bioconductor.org/packages/InteractionSet")
2101 (synopsis "Base classes for storing genomic interaction data")
2103 "This package provides the @code{GInteractions},
2104 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2105 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2107 (license license:gpl3)))
2109 (define-public r-genomicinteractions
2111 (name "r-genomicinteractions")
2116 (uri (bioconductor-uri "GenomicInteractions" version))
2119 "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy"))))
2121 `((upstream-name . "GenomicInteractions")))
2122 (build-system r-build-system)
2124 `(("r-biobase" ,r-biobase)
2125 ("r-biocgenerics" ,r-biocgenerics)
2126 ("r-data-table" ,r-data-table)
2127 ("r-dplyr" ,r-dplyr)
2128 ("r-genomeinfodb" ,r-genomeinfodb)
2129 ("r-genomicranges" ,r-genomicranges)
2130 ("r-ggplot2" ,r-ggplot2)
2131 ("r-gridextra" ,r-gridextra)
2133 ("r-igraph" ,r-igraph)
2134 ("r-interactionset" ,r-interactionset)
2135 ("r-iranges" ,r-iranges)
2136 ("r-rsamtools" ,r-rsamtools)
2137 ("r-rtracklayer" ,r-rtracklayer)
2138 ("r-s4vectors" ,r-s4vectors)
2139 ("r-stringr" ,r-stringr)))
2141 `(("r-knitr" ,r-knitr)))
2142 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2143 (synopsis "R package for handling genomic interaction data")
2145 "This R package provides tools for handling genomic interaction data,
2146 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2147 information and producing various plots and statistics.")
2148 (license license:gpl3)))
2150 (define-public r-ctc
2157 (uri (bioconductor-uri "ctc" version))
2160 "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6"))))
2161 (build-system r-build-system)
2162 (propagated-inputs `(("r-amap" ,r-amap)))
2163 (home-page "https://bioconductor.org/packages/ctc/")
2164 (synopsis "Cluster and tree conversion")
2166 "This package provides tools for exporting and importing classification
2167 trees and clusters to other programs.")
2168 (license license:gpl2)))
2170 (define-public r-goseq
2177 (uri (bioconductor-uri "goseq" version))
2180 "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym"))))
2181 (build-system r-build-system)
2183 `(("r-annotationdbi" ,r-annotationdbi)
2184 ("r-biasedurn" ,r-biasedurn)
2185 ("r-biocgenerics" ,r-biocgenerics)
2186 ("r-genelendatabase" ,r-genelendatabase)
2187 ("r-go-db" ,r-go-db)
2188 ("r-mgcv" ,r-mgcv)))
2189 (home-page "https://bioconductor.org/packages/goseq/")
2190 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2192 "This package provides tools to detect Gene Ontology and/or other user
2193 defined categories which are over/under represented in RNA-seq data.")
2194 (license license:lgpl2.0+)))
2196 (define-public r-glimma
2203 (uri (bioconductor-uri "Glimma" version))
2206 "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y"))))
2207 (properties `((upstream-name . "Glimma")))
2208 (build-system r-build-system)
2210 `(("r-edger" ,r-edger)
2211 ("r-jsonlite" ,r-jsonlite)
2212 ("r-s4vectors" ,r-s4vectors)))
2214 `(("r-knitr" ,r-knitr)))
2215 (home-page "https://github.com/Shians/Glimma")
2216 (synopsis "Interactive HTML graphics")
2218 "This package generates interactive visualisations for analysis of
2219 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2220 HTML page. The interactions are built on top of the popular static
2221 representations of analysis results in order to provide additional
2223 (license license:lgpl3)))
2225 (define-public r-rots
2232 (uri (bioconductor-uri "ROTS" version))
2235 "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm"))))
2236 (properties `((upstream-name . "ROTS")))
2237 (build-system r-build-system)
2239 `(("r-biobase" ,r-biobase)
2240 ("r-rcpp" ,r-rcpp)))
2241 (home-page "https://bioconductor.org/packages/ROTS/")
2242 (synopsis "Reproducibility-Optimized Test Statistic")
2244 "This package provides tools for calculating the
2245 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2247 (license license:gpl2+)))
2249 (define-public r-plgem
2256 (uri (bioconductor-uri "plgem" version))
2259 "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a"))))
2260 (build-system r-build-system)
2262 `(("r-biobase" ,r-biobase)
2263 ("r-mass" ,r-mass)))
2264 (home-page "http://www.genopolis.it")
2265 (synopsis "Detect differential expression in microarray and proteomics datasets")
2267 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2268 model the variance-versus-mean dependence that exists in a variety of
2269 genome-wide datasets, including microarray and proteomics data. The use of
2270 PLGEM has been shown to improve the detection of differentially expressed
2271 genes or proteins in these datasets.")
2272 (license license:gpl2)))
2274 (define-public r-inspect
2281 (uri (bioconductor-uri "INSPEcT" version))
2284 "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z"))))
2285 (properties `((upstream-name . "INSPEcT")))
2286 (build-system r-build-system)
2288 `(("r-biobase" ,r-biobase)
2289 ("r-biocgenerics" ,r-biocgenerics)
2290 ("r-biocparallel" ,r-biocparallel)
2291 ("r-deseq2" ,r-deseq2)
2292 ("r-desolve" ,r-desolve)
2293 ("r-gdata" ,r-gdata)
2294 ("r-genomeinfodb" ,r-genomeinfodb)
2295 ("r-genomicalignments" ,r-genomicalignments)
2296 ("r-genomicfeatures" ,r-genomicfeatures)
2297 ("r-genomicranges" ,r-genomicranges)
2298 ("r-iranges" ,r-iranges)
2299 ("r-kernsmooth" ,r-kernsmooth)
2300 ("r-plgem" ,r-plgem)
2302 ("r-rootsolve" ,r-rootsolve)
2303 ("r-rsamtools" ,r-rsamtools)
2304 ("r-rtracklayer" ,r-rtracklayer)
2305 ("r-s4vectors" ,r-s4vectors)
2306 ("r-shiny" ,r-shiny)
2307 ("r-summarizedexperiment" ,r-summarizedexperiment)
2308 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2309 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2311 `(("r-knitr" ,r-knitr)))
2312 (home-page "https://bioconductor.org/packages/INSPEcT")
2313 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2315 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2316 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2317 order to evaluate synthesis, processing and degradation rates and assess via
2318 modeling the rates that determines changes in mature mRNA levels.")
2319 (license license:gpl2)))
2321 (define-public r-dnabarcodes
2323 (name "r-dnabarcodes")
2328 (uri (bioconductor-uri "DNABarcodes" version))
2331 "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7"))))
2332 (properties `((upstream-name . "DNABarcodes")))
2333 (build-system r-build-system)
2336 ("r-matrix" ,r-matrix)
2337 ("r-rcpp" ,r-rcpp)))
2339 `(("r-knitr" ,r-knitr)))
2340 (home-page "https://bioconductor.org/packages/DNABarcodes")
2341 (synopsis "Create and analyze DNA barcodes")
2343 "This package offers tools to create DNA barcode sets capable of
2344 correcting insertion, deletion, and substitution errors. Existing barcodes
2345 can be analyzed regarding their minimal, maximal and average distances between
2346 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2347 demultiplexed, i.e. assigned to their original reference barcode.")
2348 (license license:gpl2)))
2350 (define-public r-ruvseq
2357 (uri (bioconductor-uri "RUVSeq" version))
2360 "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x"))))
2361 (properties `((upstream-name . "RUVSeq")))
2362 (build-system r-build-system)
2364 `(("r-biobase" ,r-biobase)
2365 ("r-edaseq" ,r-edaseq)
2366 ("r-edger" ,r-edger)
2367 ("r-mass" ,r-mass)))
2369 `(("r-knitr" ,r-knitr)))
2370 (home-page "https://github.com/drisso/RUVSeq")
2371 (synopsis "Remove unwanted variation from RNA-Seq data")
2373 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2374 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2376 (license license:artistic2.0)))
2378 (define-public r-biocneighbors
2380 (name "r-biocneighbors")
2385 (uri (bioconductor-uri "BiocNeighbors" version))
2388 "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy"))))
2389 (properties `((upstream-name . "BiocNeighbors")))
2390 (build-system r-build-system)
2392 `(("r-biocparallel" ,r-biocparallel)
2393 ("r-matrix" ,r-matrix)
2395 ("r-rcppannoy" ,r-rcppannoy)
2396 ("r-rcpphnsw" ,r-rcpphnsw)
2397 ("r-s4vectors" ,r-s4vectors)))
2399 `(("r-knitr" ,r-knitr)))
2400 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2401 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2403 "This package implements exact and approximate methods for nearest
2404 neighbor detection, in a framework that allows them to be easily switched
2405 within Bioconductor packages or workflows. The exact algorithm is implemented
2406 using pre-clustering with the k-means algorithm. Functions are also provided
2407 to search for all neighbors within a given distance. Parallelization is
2408 achieved for all methods using the BiocParallel framework.")
2409 (license license:gpl3)))
2411 (define-public r-biocsingular
2413 (name "r-biocsingular")
2418 (uri (bioconductor-uri "BiocSingular" version))
2421 "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih"))))
2422 (properties `((upstream-name . "BiocSingular")))
2423 (build-system r-build-system)
2425 `(("r-beachmat" ,r-beachmat)
2426 ("r-biocgenerics" ,r-biocgenerics)
2427 ("r-biocparallel" ,r-biocparallel)
2428 ("r-delayedarray" ,r-delayedarray)
2429 ("r-irlba" ,r-irlba)
2430 ("r-matrix" ,r-matrix)
2433 ("r-s4vectors" ,r-s4vectors)))
2435 `(("r-knitr" ,r-knitr)))
2436 (home-page "https://github.com/LTLA/BiocSingular")
2437 (synopsis "Singular value decomposition for Bioconductor packages")
2439 "This package implements exact and approximate methods for singular value
2440 decomposition and principal components analysis, in a framework that allows
2441 them to be easily switched within Bioconductor packages or workflows. Where
2442 possible, parallelization is achieved using the BiocParallel framework.")
2443 (license license:gpl3)))
2445 (define-public r-destiny
2452 (uri (bioconductor-uri "destiny" version))
2455 "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n"))))
2456 (build-system r-build-system)
2458 `(("r-biobase" ,r-biobase)
2459 ("r-biocgenerics" ,r-biocgenerics)
2460 ("r-ggplot-multistats" ,r-ggplot-multistats)
2461 ("r-ggplot2" ,r-ggplot2)
2462 ("r-ggthemes" ,r-ggthemes)
2463 ("r-irlba" ,r-irlba)
2464 ("r-knn-covertree" ,r-knn-covertree)
2465 ("r-matrix" ,r-matrix)
2466 ("r-nbconvertr" ,r-nbconvertr)
2467 ("r-pcamethods" ,r-pcamethods)
2468 ("r-proxy" ,r-proxy)
2470 ("r-rcppeigen" ,r-rcppeigen)
2471 ("r-rcpphnsw" ,r-rcpphnsw)
2472 ("r-rspectra" ,r-rspectra)
2473 ("r-scales" ,r-scales)
2474 ("r-scatterplot3d" ,r-scatterplot3d)
2475 ("r-singlecellexperiment" ,r-singlecellexperiment)
2476 ("r-smoother" ,r-smoother)
2477 ("r-summarizedexperiment" ,r-summarizedexperiment)
2478 ("r-tidyr" ,r-tidyr)
2479 ("r-tidyselect" ,r-tidyselect)
2482 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2483 (home-page "https://bioconductor.org/packages/destiny/")
2484 (synopsis "Create and plot diffusion maps")
2485 (description "This package provides tools to create and plot diffusion
2487 ;; Any version of the GPL
2488 (license license:gpl3+)))
2490 (define-public r-savr
2497 (uri (bioconductor-uri "savR" version))
2500 "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a"))))
2501 (properties `((upstream-name . "savR")))
2502 (build-system r-build-system)
2504 `(("r-ggplot2" ,r-ggplot2)
2505 ("r-gridextra" ,r-gridextra)
2506 ("r-reshape2" ,r-reshape2)
2507 ("r-scales" ,r-scales)
2509 (home-page "https://github.com/bcalder/savR")
2510 (synopsis "Parse and analyze Illumina SAV files")
2512 "This package provides tools to parse Illumina Sequence Analysis
2513 Viewer (SAV) files, access data, and generate QC plots.")
2514 (license license:agpl3+)))
2516 (define-public r-chipexoqual
2518 (name "r-chipexoqual")
2523 (uri (bioconductor-uri "ChIPexoQual" version))
2526 "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp"))))
2527 (properties `((upstream-name . "ChIPexoQual")))
2528 (build-system r-build-system)
2530 `(("r-biocparallel" ,r-biocparallel)
2531 ("r-biovizbase" ,r-biovizbase)
2532 ("r-broom" ,r-broom)
2533 ("r-data-table" ,r-data-table)
2534 ("r-dplyr" ,r-dplyr)
2535 ("r-genomeinfodb" ,r-genomeinfodb)
2536 ("r-genomicalignments" ,r-genomicalignments)
2537 ("r-genomicranges" ,r-genomicranges)
2538 ("r-ggplot2" ,r-ggplot2)
2539 ("r-hexbin" ,r-hexbin)
2540 ("r-iranges" ,r-iranges)
2541 ("r-rcolorbrewer" ,r-rcolorbrewer)
2542 ("r-rmarkdown" ,r-rmarkdown)
2543 ("r-rsamtools" ,r-rsamtools)
2544 ("r-s4vectors" ,r-s4vectors)
2545 ("r-scales" ,r-scales)
2546 ("r-viridis" ,r-viridis)))
2548 `(("r-knitr" ,r-knitr)))
2549 (home-page "https://github.com/keleslab/ChIPexoQual")
2550 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2552 "This package provides a quality control pipeline for ChIP-exo/nexus
2554 (license license:gpl2+)))
2556 (define-public r-copynumber
2558 (name "r-copynumber")
2562 (uri (bioconductor-uri "copynumber" version))
2565 "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my"))))
2566 (build-system r-build-system)
2568 `(("r-s4vectors" ,r-s4vectors)
2569 ("r-iranges" ,r-iranges)
2570 ("r-genomicranges" ,r-genomicranges)
2571 ("r-biocgenerics" ,r-biocgenerics)))
2572 (home-page "https://bioconductor.org/packages/copynumber")
2573 (synopsis "Segmentation of single- and multi-track copy number data")
2575 "This package segments single- and multi-track copy number data by a
2576 penalized least squares regression method.")
2577 (license license:artistic2.0)))
2579 (define-public r-dnacopy
2586 (uri (bioconductor-uri "DNAcopy" version))
2589 "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza"))))
2590 (properties `((upstream-name . "DNAcopy")))
2591 (build-system r-build-system)
2592 (native-inputs `(("gfortran" ,gfortran)))
2593 (home-page "https://bioconductor.org/packages/DNAcopy")
2594 (synopsis "DNA copy number data analysis")
2596 "This package implements the @dfn{circular binary segmentation} (CBS)
2597 algorithm to segment DNA copy number data and identify genomic regions with
2598 abnormal copy number.")
2599 (license license:gpl2+)))
2601 ;; This is a CRAN package, but it uncharacteristically depends on a
2602 ;; Bioconductor package.
2603 (define-public r-htscluster
2605 (name "r-htscluster")
2610 (uri (cran-uri "HTSCluster" version))
2613 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2614 (properties `((upstream-name . "HTSCluster")))
2615 (build-system r-build-system)
2617 `(("r-capushe" ,r-capushe)
2618 ("r-edger" ,r-edger)
2619 ("r-plotrix" ,r-plotrix)))
2620 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2621 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2623 "This package provides a Poisson mixture model is implemented to cluster
2624 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2625 estimation is performed using either the EM or CEM algorithm, and the slope
2626 heuristics are used for model selection (i.e., to choose the number of
2628 (license license:gpl3+)))
2630 (define-public r-deds
2637 (uri (bioconductor-uri "DEDS" version))
2640 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2641 (properties `((upstream-name . "DEDS")))
2642 (build-system r-build-system)
2643 (home-page "https://bioconductor.org/packages/DEDS/")
2644 (synopsis "Differential expression via distance summary for microarray data")
2646 "This library contains functions that calculate various statistics of
2647 differential expression for microarray data, including t statistics, fold
2648 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2649 also implements a new methodology called DEDS (Differential Expression via
2650 Distance Summary), which selects differentially expressed genes by integrating
2651 and summarizing a set of statistics using a weighted distance approach.")
2652 ;; Any version of the LGPL.
2653 (license license:lgpl3+)))
2655 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2657 (define-public r-nbpseq
2664 (uri (cran-uri "NBPSeq" version))
2667 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2668 (properties `((upstream-name . "NBPSeq")))
2669 (build-system r-build-system)
2671 `(("r-qvalue" ,r-qvalue)))
2672 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2673 (synopsis "Negative binomial models for RNA-Seq data")
2675 "This package provides negative binomial models for two-group comparisons
2676 and regression inferences from RNA-sequencing data.")
2677 (license license:gpl2)))
2679 (define-public r-ebseq
2686 (uri (bioconductor-uri "EBSeq" version))
2689 "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f"))))
2690 (properties `((upstream-name . "EBSeq")))
2691 (build-system r-build-system)
2693 `(("r-blockmodeling" ,r-blockmodeling)
2694 ("r-gplots" ,r-gplots)
2695 ("r-testthat" ,r-testthat)))
2696 (home-page "https://bioconductor.org/packages/EBSeq")
2697 (synopsis "Differential expression analysis of RNA-seq data")
2699 "This package provides tools for differential expression analysis at both
2700 gene and isoform level using RNA-seq data")
2701 (license license:artistic2.0)))
2703 (define-public r-karyoploter
2705 (name "r-karyoploter")
2709 (uri (bioconductor-uri "karyoploteR" version))
2712 "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs"))))
2713 (build-system r-build-system)
2715 `(("r-annotationdbi" ,r-annotationdbi)
2716 ("r-bamsignals" ,r-bamsignals)
2717 ("r-bezier" ,r-bezier)
2718 ("r-biovizbase" ,r-biovizbase)
2719 ("r-digest" ,r-digest)
2720 ("r-genomeinfodb" ,r-genomeinfodb)
2721 ("r-genomicfeatures" ,r-genomicfeatures)
2722 ("r-genomicranges" ,r-genomicranges)
2723 ("r-iranges" ,r-iranges)
2724 ("r-memoise" ,r-memoise)
2725 ("r-regioner" ,r-regioner)
2726 ("r-rsamtools" ,r-rsamtools)
2727 ("r-rtracklayer" ,r-rtracklayer)
2728 ("r-s4vectors" ,r-s4vectors)
2729 ("r-variantannotation" ,r-variantannotation)))
2731 `(("r-knitr" ,r-knitr)))
2732 (home-page "https://bioconductor.org/packages/karyoploteR/")
2733 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2734 (description "This package creates karyotype plots of arbitrary genomes and
2735 offers a complete set of functions to plot arbitrary data on them. It mimicks
2736 many R base graphics functions coupling them with a coordinate change function
2737 automatically mapping the chromosome and data coordinates into the plot
2739 (license license:artistic2.0)))
2741 (define-public r-lpsymphony
2743 (name "r-lpsymphony")
2748 (uri (bioconductor-uri "lpsymphony" version))
2751 "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4"))))
2752 (build-system r-build-system)
2756 `(("pkg-config" ,pkg-config)
2757 ("r-knitr" ,r-knitr)))
2758 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2759 (synopsis "Symphony integer linear programming solver in R")
2761 "This package was derived from Rsymphony. The package provides an R
2762 interface to SYMPHONY, a linear programming solver written in C++. The main
2763 difference between this package and Rsymphony is that it includes the solver
2764 source code, while Rsymphony expects to find header and library files on the
2765 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2766 to install interface to SYMPHONY.")
2767 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2768 ;; lpsimphony is released under the same terms.
2769 (license license:epl1.0)))
2771 (define-public r-ihw
2778 (uri (bioconductor-uri "IHW" version))
2781 "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j"))))
2782 (properties `((upstream-name . "IHW")))
2783 (build-system r-build-system)
2785 `(("r-biocgenerics" ,r-biocgenerics)
2786 ("r-fdrtool" ,r-fdrtool)
2787 ("r-lpsymphony" ,r-lpsymphony)
2788 ("r-slam" ,r-slam)))
2790 `(("r-knitr" ,r-knitr)))
2791 (home-page "https://bioconductor.org/packages/IHW")
2792 (synopsis "Independent hypothesis weighting")
2794 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2795 procedure that increases power compared to the method of Benjamini and
2796 Hochberg by assigning data-driven weights to each hypothesis. The input to
2797 IHW is a two-column table of p-values and covariates. The covariate can be
2798 any continuous-valued or categorical variable that is thought to be
2799 informative on the statistical properties of each hypothesis test, while it is
2800 independent of the p-value under the null hypothesis.")
2801 (license license:artistic2.0)))
2803 (define-public r-icobra
2810 (uri (bioconductor-uri "iCOBRA" version))
2813 "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1"))))
2814 (properties `((upstream-name . "iCOBRA")))
2815 (build-system r-build-system)
2817 `(("r-dplyr" ,r-dplyr)
2819 ("r-ggplot2" ,r-ggplot2)
2820 ("r-limma" ,r-limma)
2821 ("r-reshape2" ,r-reshape2)
2823 ("r-scales" ,r-scales)
2824 ("r-shiny" ,r-shiny)
2825 ("r-shinybs" ,r-shinybs)
2826 ("r-shinydashboard" ,r-shinydashboard)
2827 ("r-upsetr" ,r-upsetr)))
2829 `(("r-knitr" ,r-knitr)))
2830 (home-page "https://bioconductor.org/packages/iCOBRA")
2831 (synopsis "Comparison and visualization of ranking and assignment methods")
2833 "This package provides functions for calculation and visualization of
2834 performance metrics for evaluation of ranking and binary
2835 classification (assignment) methods. It also contains a Shiny application for
2836 interactive exploration of results.")
2837 (license license:gpl2+)))
2839 (define-public r-mast
2846 (uri (bioconductor-uri "MAST" version))
2849 "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr"))))
2850 (properties `((upstream-name . "MAST")))
2851 (build-system r-build-system)
2853 `(("r-abind" ,r-abind)
2854 ("r-biobase" ,r-biobase)
2855 ("r-biocgenerics" ,r-biocgenerics)
2856 ("r-data-table" ,r-data-table)
2857 ("r-ggplot2" ,r-ggplot2)
2859 ("r-progress" ,r-progress)
2860 ("r-reshape2" ,r-reshape2)
2861 ("r-s4vectors" ,r-s4vectors)
2862 ("r-singlecellexperiment" ,r-singlecellexperiment)
2863 ("r-stringr" ,r-stringr)
2864 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2866 `(("r-knitr" ,r-knitr)))
2867 (home-page "https://github.com/RGLab/MAST/")
2868 (synopsis "Model-based analysis of single cell transcriptomics")
2870 "This package provides methods and models for handling zero-inflated
2871 single cell assay data.")
2872 (license license:gpl2+)))
2874 (define-public r-monocle
2881 (uri (bioconductor-uri "monocle" version))
2884 "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd"))))
2885 (build-system r-build-system)
2887 `(("r-biobase" ,r-biobase)
2888 ("r-biocgenerics" ,r-biocgenerics)
2889 ("r-biocviews" ,r-biocviews)
2890 ("r-cluster" ,r-cluster)
2891 ("r-combinat" ,r-combinat)
2892 ("r-ddrtree" ,r-ddrtree)
2893 ("r-densityclust" ,r-densityclust)
2894 ("r-dplyr" ,r-dplyr)
2895 ("r-fastica" ,r-fastica)
2896 ("r-ggplot2" ,r-ggplot2)
2897 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2898 ("r-igraph" ,r-igraph)
2899 ("r-irlba" ,r-irlba)
2900 ("r-limma" ,r-limma)
2902 ("r-matrix" ,r-matrix)
2903 ("r-matrixstats" ,r-matrixstats)
2904 ("r-pheatmap" ,r-pheatmap)
2906 ("r-proxy" ,r-proxy)
2907 ("r-qlcmatrix" ,r-qlcmatrix)
2910 ("r-reshape2" ,r-reshape2)
2911 ("r-rtsne" ,r-rtsne)
2913 ("r-stringr" ,r-stringr)
2914 ("r-tibble" ,r-tibble)
2916 ("r-viridis" ,r-viridis)))
2918 `(("r-knitr" ,r-knitr)))
2919 (home-page "https://bioconductor.org/packages/monocle")
2920 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2922 "Monocle performs differential expression and time-series analysis for
2923 single-cell expression experiments. It orders individual cells according to
2924 progress through a biological process, without knowing ahead of time which
2925 genes define progress through that process. Monocle also performs
2926 differential expression analysis, clustering, visualization, and other useful
2927 tasks on single cell expression data. It is designed to work with RNA-Seq and
2928 qPCR data, but could be used with other types as well.")
2929 (license license:artistic2.0)))
2931 (define-public r-monocle3
2939 (url "https://github.com/cole-trapnell-lab/monocle3")
2941 (file-name (git-file-name name version))
2944 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2945 (build-system r-build-system)
2947 `(("r-biobase" ,r-biobase)
2948 ("r-biocgenerics" ,r-biocgenerics)
2949 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2950 ("r-dplyr" ,r-dplyr)
2951 ("r-ggplot2" ,r-ggplot2)
2952 ("r-ggrepel" ,r-ggrepel)
2954 ("r-htmlwidgets" ,r-htmlwidgets)
2955 ("r-igraph" ,r-igraph)
2956 ("r-irlba" ,r-irlba)
2957 ("r-limma" ,r-limma)
2958 ("r-lmtest" ,r-lmtest)
2960 ("r-matrix" ,r-matrix)
2961 ("r-matrix-utils" ,r-matrix-utils)
2962 ("r-pbapply" ,r-pbapply)
2963 ("r-pbmcapply" ,r-pbmcapply)
2964 ("r-pheatmap" ,r-pheatmap)
2965 ("r-plotly" ,r-plotly)
2967 ("r-proxy" ,r-proxy)
2969 ("r-purrr" ,r-purrr)
2972 ("r-rcppparallel" ,r-rcppparallel)
2973 ("r-reshape2" ,r-reshape2)
2974 ("r-reticulate" ,r-reticulate)
2975 ("r-rhpcblasctl" ,r-rhpcblasctl)
2976 ("r-rtsne" ,r-rtsne)
2977 ("r-shiny" ,r-shiny)
2979 ("r-spdep" ,r-spdep)
2980 ("r-speedglm" ,r-speedglm)
2981 ("r-stringr" ,r-stringr)
2982 ("r-singlecellexperiment" ,r-singlecellexperiment)
2983 ("r-tibble" ,r-tibble)
2984 ("r-tidyr" ,r-tidyr)
2986 ("r-viridis" ,r-viridis)))
2987 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2988 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2990 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2991 (license license:expat)))
2993 (define-public r-noiseq
3000 (uri (bioconductor-uri "NOISeq" version))
3003 "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33"))))
3004 (properties `((upstream-name . "NOISeq")))
3005 (build-system r-build-system)
3007 `(("r-biobase" ,r-biobase)
3008 ("r-matrix" ,r-matrix)))
3009 (home-page "https://bioconductor.org/packages/NOISeq")
3010 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3012 "This package provides tools to support the analysis of RNA-seq
3013 expression data or other similar kind of data. It provides exploratory plots
3014 to evaluate saturation, count distribution, expression per chromosome, type of
3015 detected features, features length, etc. It also supports the analysis of
3016 differential expression between two experimental conditions with no parametric
3018 (license license:artistic2.0)))
3020 (define-public r-scdd
3027 (uri (bioconductor-uri "scDD" version))
3030 "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx"))))
3031 (properties `((upstream-name . "scDD")))
3032 (build-system r-build-system)
3035 ("r-biocparallel" ,r-biocparallel)
3036 ("r-ebseq" ,r-ebseq)
3037 ("r-fields" ,r-fields)
3038 ("r-ggplot2" ,r-ggplot2)
3039 ("r-mclust" ,r-mclust)
3040 ("r-outliers" ,r-outliers)
3041 ("r-s4vectors" ,r-s4vectors)
3042 ("r-scran" ,r-scran)
3043 ("r-singlecellexperiment" ,r-singlecellexperiment)
3044 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3046 `(("r-knitr" ,r-knitr)))
3047 (home-page "https://github.com/kdkorthauer/scDD")
3048 (synopsis "Mixture modeling of single-cell RNA-seq data")
3050 "This package implements a method to analyze single-cell RNA-seq data
3051 utilizing flexible Dirichlet Process mixture models. Genes with differential
3052 distributions of expression are classified into several interesting patterns
3053 of differences between two conditions. The package also includes functions
3054 for simulating data with these patterns from negative binomial
3056 (license license:gpl2)))
3058 (define-public r-scone
3065 (uri (bioconductor-uri "scone" version))
3068 "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g"))))
3069 (build-system r-build-system)
3071 `(("r-aroma-light" ,r-aroma-light)
3072 ("r-biocparallel" ,r-biocparallel)
3074 ("r-class" ,r-class)
3075 ("r-cluster" ,r-cluster)
3076 ("r-compositions" ,r-compositions)
3077 ("r-diptest" ,r-diptest)
3078 ("r-edger" ,r-edger)
3080 ("r-gplots" ,r-gplots)
3081 ("r-hexbin" ,r-hexbin)
3082 ("r-limma" ,r-limma)
3083 ("r-matrixstats" ,r-matrixstats)
3084 ("r-mixtools" ,r-mixtools)
3085 ("r-rarpack" ,r-rarpack)
3086 ("r-rcolorbrewer" ,r-rcolorbrewer)
3087 ("r-rhdf5" ,r-rhdf5)
3088 ("r-ruvseq" ,r-ruvseq)
3089 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3091 `(("r-knitr" ,r-knitr)))
3092 (home-page "https://bioconductor.org/packages/scone")
3093 (synopsis "Single cell overview of normalized expression data")
3095 "SCONE is an R package for comparing and ranking the performance of
3096 different normalization schemes for single-cell RNA-seq and other
3097 high-throughput analyses.")
3098 (license license:artistic2.0)))
3100 (define-public r-geoquery
3107 (uri (bioconductor-uri "GEOquery" version))
3110 "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m"))))
3111 (properties `((upstream-name . "GEOquery")))
3112 (build-system r-build-system)
3114 `(("r-biobase" ,r-biobase)
3115 ("r-dplyr" ,r-dplyr)
3117 ("r-limma" ,r-limma)
3118 ("r-magrittr" ,r-magrittr)
3119 ("r-readr" ,r-readr)
3120 ("r-tidyr" ,r-tidyr)
3121 ("r-xml2" ,r-xml2)))
3123 `(("r-knitr" ,r-knitr)))
3124 (home-page "https://github.com/seandavi/GEOquery/")
3125 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3127 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3128 microarray data. Given the rich and varied nature of this resource, it is
3129 only natural to want to apply BioConductor tools to these data. GEOquery is
3130 the bridge between GEO and BioConductor.")
3131 (license license:gpl2)))
3133 (define-public r-illuminaio
3135 (name "r-illuminaio")
3140 (uri (bioconductor-uri "illuminaio" version))
3143 "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c"))))
3144 (build-system r-build-system)
3146 `(("r-base64" ,r-base64)))
3147 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3148 (synopsis "Parse Illumina microarray output files")
3150 "This package provides tools for parsing Illumina's microarray output
3151 files, including IDAT.")
3152 (license license:gpl2)))
3154 (define-public r-siggenes
3161 (uri (bioconductor-uri "siggenes" version))
3164 "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy"))))
3165 (build-system r-build-system)
3167 `(("r-biobase" ,r-biobase)
3168 ("r-multtest" ,r-multtest)
3169 ("r-scrime" ,r-scrime)))
3170 (home-page "https://bioconductor.org/packages/siggenes/")
3172 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3174 "This package provides tools for the identification of differentially
3175 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3176 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3177 Bayes Analyses of Microarrays} (EBAM).")
3178 (license license:lgpl2.0+)))
3180 (define-public r-bumphunter
3182 (name "r-bumphunter")
3187 (uri (bioconductor-uri "bumphunter" version))
3190 "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq"))))
3191 (build-system r-build-system)
3193 `(("r-annotationdbi" ,r-annotationdbi)
3194 ("r-biocgenerics" ,r-biocgenerics)
3195 ("r-dorng" ,r-dorng)
3196 ("r-foreach" ,r-foreach)
3197 ("r-genomeinfodb" ,r-genomeinfodb)
3198 ("r-genomicfeatures" ,r-genomicfeatures)
3199 ("r-genomicranges" ,r-genomicranges)
3200 ("r-iranges" ,r-iranges)
3201 ("r-iterators" ,r-iterators)
3202 ("r-limma" ,r-limma)
3203 ("r-locfit" ,r-locfit)
3204 ("r-matrixstats" ,r-matrixstats)
3205 ("r-s4vectors" ,r-s4vectors)))
3206 (home-page "https://github.com/ririzarr/bumphunter")
3207 (synopsis "Find bumps in genomic data")
3209 "This package provides tools for finding bumps in genomic data in order
3210 to identify differentially methylated regions in epigenetic epidemiology
3212 (license license:artistic2.0)))
3214 (define-public r-minfi
3221 (uri (bioconductor-uri "minfi" version))
3224 "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w"))))
3225 (build-system r-build-system)
3227 `(("r-beanplot" ,r-beanplot)
3228 ("r-biobase" ,r-biobase)
3229 ("r-biocgenerics" ,r-biocgenerics)
3230 ("r-biocparallel" ,r-biocparallel)
3231 ("r-biostrings" ,r-biostrings)
3232 ("r-bumphunter" ,r-bumphunter)
3233 ("r-data-table" ,r-data-table)
3234 ("r-delayedarray" ,r-delayedarray)
3235 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3236 ("r-genefilter" ,r-genefilter)
3237 ("r-genomeinfodb" ,r-genomeinfodb)
3238 ("r-genomicranges" ,r-genomicranges)
3239 ("r-geoquery" ,r-geoquery)
3240 ("r-hdf5array" ,r-hdf5array)
3241 ("r-illuminaio" ,r-illuminaio)
3242 ("r-iranges" ,r-iranges)
3243 ("r-lattice" ,r-lattice)
3244 ("r-limma" ,r-limma)
3246 ("r-mclust" ,r-mclust)
3248 ("r-nor1mix" ,r-nor1mix)
3249 ("r-preprocesscore" ,r-preprocesscore)
3250 ("r-quadprog" ,r-quadprog)
3251 ("r-rcolorbrewer" ,r-rcolorbrewer)
3252 ("r-reshape" ,r-reshape)
3253 ("r-s4vectors" ,r-s4vectors)
3254 ("r-siggenes" ,r-siggenes)
3255 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3257 `(("r-knitr" ,r-knitr)))
3258 (home-page "https://github.com/hansenlab/minfi")
3259 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3261 "This package provides tools to analyze and visualize Illumina Infinium
3262 methylation arrays.")
3263 (license license:artistic2.0)))
3265 (define-public r-methylumi
3267 (name "r-methylumi")
3272 (uri (bioconductor-uri "methylumi" version))
3275 "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr"))))
3276 (build-system r-build-system)
3278 `(("r-annotate" ,r-annotate)
3279 ("r-annotationdbi" ,r-annotationdbi)
3280 ("r-biobase" ,r-biobase)
3281 ("r-biocgenerics" ,r-biocgenerics)
3282 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3283 ("r-genefilter" ,r-genefilter)
3284 ("r-genomeinfodb" ,r-genomeinfodb)
3285 ("r-genomicranges" ,r-genomicranges)
3286 ("r-ggplot2" ,r-ggplot2)
3287 ("r-illuminaio" ,r-illuminaio)
3288 ("r-iranges" ,r-iranges)
3289 ("r-lattice" ,r-lattice)
3290 ("r-matrixstats" ,r-matrixstats)
3291 ("r-minfi" ,r-minfi)
3292 ("r-reshape2" ,r-reshape2)
3293 ("r-s4vectors" ,r-s4vectors)
3294 ("r-scales" ,r-scales)
3295 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3297 `(("r-knitr" ,r-knitr)))
3298 (home-page "https://bioconductor.org/packages/methylumi")
3299 (synopsis "Handle Illumina methylation data")
3301 "This package provides classes for holding and manipulating Illumina
3302 methylation data. Based on eSet, it can contain MIAME information, sample
3303 information, feature information, and multiple matrices of data. An
3304 \"intelligent\" import function, methylumiR can read the Illumina text files
3305 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3306 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3307 background correction, and quality control features for GoldenGate, Infinium,
3308 and Infinium HD arrays are also included.")
3309 (license license:gpl2)))
3311 (define-public r-lumi
3318 (uri (bioconductor-uri "lumi" version))
3321 "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9"))))
3322 (build-system r-build-system)
3324 `(("r-affy" ,r-affy)
3325 ("r-annotate" ,r-annotate)
3326 ("r-annotationdbi" ,r-annotationdbi)
3327 ("r-biobase" ,r-biobase)
3329 ("r-genomicfeatures" ,r-genomicfeatures)
3330 ("r-genomicranges" ,r-genomicranges)
3331 ("r-kernsmooth" ,r-kernsmooth)
3332 ("r-lattice" ,r-lattice)
3334 ("r-methylumi" ,r-methylumi)
3336 ("r-nleqslv" ,r-nleqslv)
3337 ("r-preprocesscore" ,r-preprocesscore)
3338 ("r-rsqlite" ,r-rsqlite)))
3339 (home-page "https://bioconductor.org/packages/lumi")
3340 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3342 "The lumi package provides an integrated solution for the Illumina
3343 microarray data analysis. It includes functions of Illumina
3344 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3345 variance stabilization, normalization and gene annotation at the probe level.
3346 It also includes the functions of processing Illumina methylation microarrays,
3347 especially Illumina Infinium methylation microarrays.")
3348 (license license:lgpl2.0+)))
3350 (define-public r-linnorm
3357 (uri (bioconductor-uri "Linnorm" version))
3360 "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp"))))
3361 (properties `((upstream-name . "Linnorm")))
3362 (build-system r-build-system)
3364 `(("r-amap" ,r-amap)
3365 ("r-apcluster" ,r-apcluster)
3366 ("r-ellipse" ,r-ellipse)
3367 ("r-fastcluster" ,r-fastcluster)
3369 ("r-ggdendro" ,r-ggdendro)
3370 ("r-ggplot2" ,r-ggplot2)
3371 ("r-gmodels" ,r-gmodels)
3372 ("r-igraph" ,r-igraph)
3373 ("r-limma" ,r-limma)
3375 ("r-mclust" ,r-mclust)
3377 ("r-rcpparmadillo" ,r-rcpparmadillo)
3378 ("r-rtsne" ,r-rtsne)
3379 ("r-statmod" ,r-statmod)
3380 ("r-vegan" ,r-vegan)
3383 `(("r-knitr" ,r-knitr)))
3384 (home-page "http://www.jjwanglab.org/Linnorm/")
3385 (synopsis "Linear model and normality based transformation method")
3387 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3388 count data or any large scale count data. It transforms such datasets for
3389 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3390 the following pipelines are implemented:
3393 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3394 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3395 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3396 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3397 @item Differential expression analysis or differential peak detection using
3398 limma (@code{Linnorm.limma})
3399 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3400 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3401 @item Stable gene selection for scRNA-seq data; for users without or who do
3402 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3403 @item Data imputation (@code{Linnorm.DataImput}).
3406 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3407 @code{RnaXSim} function is included for simulating RNA-seq data for the
3408 evaluation of DEG analysis methods.")
3409 (license license:expat)))
3411 (define-public r-ioniser
3418 (uri (bioconductor-uri "IONiseR" version))
3421 "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w"))))
3422 (properties `((upstream-name . "IONiseR")))
3423 (build-system r-build-system)
3425 `(("r-biocgenerics" ,r-biocgenerics)
3426 ("r-biocparallel" ,r-biocparallel)
3427 ("r-biostrings" ,r-biostrings)
3428 ("r-bit64" ,r-bit64)
3429 ("r-dplyr" ,r-dplyr)
3430 ("r-ggplot2" ,r-ggplot2)
3431 ("r-magrittr" ,r-magrittr)
3432 ("r-rhdf5" ,r-rhdf5)
3433 ("r-shortread" ,r-shortread)
3434 ("r-stringr" ,r-stringr)
3435 ("r-tibble" ,r-tibble)
3436 ("r-tidyr" ,r-tidyr)
3437 ("r-xvector" ,r-xvector)))
3439 `(("r-knitr" ,r-knitr)))
3440 (home-page "https://bioconductor.org/packages/IONiseR/")
3441 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3443 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3444 MinION data. It extracts summary statistics from a set of fast5 files and can
3445 be used either before or after base calling. In addition to standard
3446 summaries of the read-types produced, it provides a number of plots for
3447 visualising metrics relative to experiment run time or spatially over the
3448 surface of a flowcell.")
3449 (license license:expat)))
3451 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3452 (define-public r-gkmsvm
3459 (uri (cran-uri "gkmSVM" version))
3462 "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p"))))
3463 (properties `((upstream-name . "gkmSVM")))
3464 (build-system r-build-system)
3466 `(("r-kernlab" ,r-kernlab)
3469 ("r-seqinr" ,r-seqinr)))
3470 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3471 (synopsis "Gapped-kmer support vector machine")
3473 "This R package provides tools for training gapped-kmer SVM classifiers
3474 for DNA and protein sequences. This package supports several sequence
3475 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3476 (license license:gpl2+)))
3478 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3479 (define-public r-mutoss
3486 (uri (cran-uri "mutoss" version))
3489 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3490 (properties `((upstream-name . "mutoss")))
3491 (build-system r-build-system)
3493 `(("r-multcomp" ,r-multcomp)
3494 ("r-multtest" ,r-multtest)
3495 ("r-mvtnorm" ,r-mvtnorm)
3496 ("r-plotrix" ,r-plotrix)))
3497 (home-page "https://github.com/kornl/mutoss/")
3498 (synopsis "Unified multiple testing procedures")
3500 "This package is designed to ease the application and comparison of
3501 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3502 are standardized and usable by the accompanying mutossGUI package.")
3503 ;; Any version of the GPL.
3504 (license (list license:gpl2+ license:gpl3+))))
3506 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3507 ;; from Bioconductor, so we put it here.
3508 (define-public r-metap
3515 (uri (cran-uri "metap" version))
3518 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3519 (build-system r-build-system)
3521 `(("r-lattice" ,r-lattice)
3522 ("r-mutoss" ,r-mutoss)
3523 ("r-rdpack" ,r-rdpack)
3524 ("r-tfisher" ,r-tfisher)))
3525 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3526 (synopsis "Meta-analysis of significance values")
3528 "The canonical way to perform meta-analysis involves using effect sizes.
3529 When they are not available this package provides a number of methods for
3530 meta-analysis of significance values including the methods of Edgington,
3531 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3532 published results; and a routine for graphical display.")
3533 (license license:gpl2)))
3535 (define-public r-triform
3542 (uri (bioconductor-uri "triform" version))
3545 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3546 (build-system r-build-system)
3548 `(("r-biocgenerics" ,r-biocgenerics)
3549 ("r-iranges" ,r-iranges)
3550 ("r-yaml" ,r-yaml)))
3551 (home-page "https://bioconductor.org/packages/triform/")
3552 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3554 "The Triform algorithm uses model-free statistics to identify peak-like
3555 distributions of TF ChIP sequencing reads, taking advantage of an improved
3556 peak definition in combination with known profile characteristics.")
3557 (license license:gpl2)))
3559 (define-public r-varianttools
3561 (name "r-varianttools")
3566 (uri (bioconductor-uri "VariantTools" version))
3569 "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx"))))
3570 (properties `((upstream-name . "VariantTools")))
3571 (build-system r-build-system)
3573 `(("r-biobase" ,r-biobase)
3574 ("r-biocgenerics" ,r-biocgenerics)
3575 ("r-biocparallel" ,r-biocparallel)
3576 ("r-biostrings" ,r-biostrings)
3577 ("r-bsgenome" ,r-bsgenome)
3578 ("r-genomeinfodb" ,r-genomeinfodb)
3579 ("r-genomicfeatures" ,r-genomicfeatures)
3580 ("r-genomicranges" ,r-genomicranges)
3581 ("r-iranges" ,r-iranges)
3582 ("r-matrix" ,r-matrix)
3583 ("r-rsamtools" ,r-rsamtools)
3584 ("r-rtracklayer" ,r-rtracklayer)
3585 ("r-s4vectors" ,r-s4vectors)
3586 ("r-variantannotation" ,r-variantannotation)))
3587 (home-page "https://bioconductor.org/packages/VariantTools/")
3588 (synopsis "Tools for exploratory analysis of variant calls")
3590 "Explore, diagnose, and compare variant calls using filters. The
3591 VariantTools package supports a workflow for loading data, calling single
3592 sample variants and tumor-specific somatic mutations or other sample-specific
3593 variant types (e.g., RNA editing). Most of the functions operate on
3594 alignments (BAM files) or datasets of called variants. The user is expected
3595 to have already aligned the reads with a separate tool, e.g., GSNAP via
3597 (license license:artistic2.0)))
3599 (define-public r-heatplus
3606 (uri (bioconductor-uri "Heatplus" version))
3609 "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw"))))
3610 (properties `((upstream-name . "Heatplus")))
3611 (build-system r-build-system)
3613 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3614 (home-page "https://github.com/alexploner/Heatplus")
3615 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3617 "This package provides tools to display a rectangular heatmap (intensity
3618 plot) of a data matrix. By default, both samples (columns) and features (row)
3619 of the matrix are sorted according to a hierarchical clustering, and the
3620 corresponding dendrogram is plotted. Optionally, panels with additional
3621 information about samples and features can be added to the plot.")
3622 (license license:gpl2+)))
3624 (define-public r-gosemsim
3631 (uri (bioconductor-uri "GOSemSim" version))
3634 "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln"))))
3635 (properties `((upstream-name . "GOSemSim")))
3636 (build-system r-build-system)
3638 `(("r-annotationdbi" ,r-annotationdbi)
3639 ("r-go-db" ,r-go-db)
3640 ("r-rcpp" ,r-rcpp)))
3642 `(("r-knitr" ,r-knitr)))
3643 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3644 (synopsis "GO-terms semantic similarity measures")
3646 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3647 quantitative ways to compute similarities between genes and gene groups, and
3648 have became important basis for many bioinformatics analysis approaches.
3649 GOSemSim is an R package for semantic similarity computation among GO terms,
3650 sets of GO terms, gene products and gene clusters.")
3651 (license license:artistic2.0)))
3653 (define-public r-anota
3660 (uri (bioconductor-uri "anota" version))
3663 "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm"))))
3664 (build-system r-build-system)
3666 `(("r-multtest" ,r-multtest)
3667 ("r-qvalue" ,r-qvalue)))
3668 (home-page "https://bioconductor.org/packages/anota/")
3669 (synopsis "Analysis of translational activity")
3671 "Genome wide studies of translational control is emerging as a tool to
3672 study various biological conditions. The output from such analysis is both
3673 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3674 involved in translation (the actively translating mRNA level) for each mRNA.
3675 The standard analysis of such data strives towards identifying differential
3676 translational between two or more sample classes - i.e. differences in
3677 actively translated mRNA levels that are independent of underlying differences
3678 in cytosolic mRNA levels. This package allows for such analysis using partial
3679 variances and the random variance model. As 10s of thousands of mRNAs are
3680 analyzed in parallel the library performs a number of tests to assure that
3681 the data set is suitable for such analysis.")
3682 (license license:gpl3)))
3684 (define-public r-sigpathway
3686 (name "r-sigpathway")
3691 (uri (bioconductor-uri "sigPathway" version))
3694 "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5"))))
3695 (properties `((upstream-name . "sigPathway")))
3696 (build-system r-build-system)
3697 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3698 (synopsis "Pathway analysis")
3700 "This package is used to conduct pathway analysis by calculating the NT_k
3701 and NE_k statistics in a statistical framework for determining whether a
3702 specified group of genes for a pathway has a coordinated association with a
3703 phenotype of interest.")
3704 (license license:gpl2)))
3706 (define-public r-fgsea
3713 (uri (bioconductor-uri "fgsea" version))
3716 "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc"))))
3717 (build-system r-build-system)
3720 ("r-biocparallel" ,r-biocparallel)
3721 ("r-data-table" ,r-data-table)
3722 ("r-fastmatch" ,r-fastmatch)
3723 ("r-ggplot2" ,r-ggplot2)
3724 ("r-gridextra" ,r-gridextra)
3725 ("r-matrix" ,r-matrix)
3726 ("r-rcpp" ,r-rcpp)))
3728 `(("r-knitr" ,r-knitr)))
3729 (home-page "https://github.com/ctlab/fgsea/")
3730 (synopsis "Fast gene set enrichment analysis")
3732 "The package implements an algorithm for fast gene set enrichment
3733 analysis. Using the fast algorithm makes more permutations and gets
3734 more fine grained p-values, which allows using accurate standard approaches
3735 to multiple hypothesis correction.")
3736 (license license:expat)))
3738 (define-public r-dose
3745 (uri (bioconductor-uri "DOSE" version))
3748 "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8"))))
3749 (properties `((upstream-name . "DOSE")))
3750 (build-system r-build-system)
3752 `(("r-annotationdbi" ,r-annotationdbi)
3753 ("r-biocparallel" ,r-biocparallel)
3754 ("r-do-db" ,r-do-db)
3755 ("r-fgsea" ,r-fgsea)
3756 ("r-ggplot2" ,r-ggplot2)
3757 ("r-gosemsim" ,r-gosemsim)
3758 ("r-qvalue" ,r-qvalue)
3759 ("r-reshape2" ,r-reshape2)))
3761 `(("r-knitr" ,r-knitr)))
3762 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3763 (synopsis "Disease ontology semantic and enrichment analysis")
3765 "This package implements five methods proposed by Resnik, Schlicker,
3766 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3767 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3768 including hypergeometric model and gene set enrichment analysis are also
3769 implemented for discovering disease associations of high-throughput biological
3771 (license license:artistic2.0)))
3773 (define-public r-enrichplot
3775 (name "r-enrichplot")
3780 (uri (bioconductor-uri "enrichplot" version))
3783 "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7"))))
3784 (build-system r-build-system)
3786 `(("r-annotationdbi" ,r-annotationdbi)
3787 ("r-cowplot" ,r-cowplot)
3789 ("r-europepmc" ,r-europepmc)
3790 ("r-ggplot2" ,r-ggplot2)
3791 ("r-ggplotify" ,r-ggplotify)
3792 ("r-ggraph" ,r-ggraph)
3793 ("r-ggridges" ,r-ggridges)
3794 ("r-gosemsim" ,r-gosemsim)
3795 ("r-gridextra" ,r-gridextra)
3796 ("r-igraph" ,r-igraph)
3798 ("r-purrr" ,r-purrr)
3799 ("r-rcolorbrewer" ,r-rcolorbrewer)
3800 ("r-reshape2" ,r-reshape2)
3801 ("r-scatterpie" ,r-scatterpie)))
3803 `(("r-knitr" ,r-knitr)))
3804 (home-page "https://github.com/GuangchuangYu/enrichplot")
3805 (synopsis "Visualization of functional enrichment result")
3807 "The enrichplot package implements several visualization methods for
3808 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3809 All the visualization methods are developed based on ggplot2 graphics.")
3810 (license license:artistic2.0)))
3812 (define-public r-clusterprofiler
3814 (name "r-clusterprofiler")
3819 (uri (bioconductor-uri "clusterProfiler" version))
3822 "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb"))))
3824 `((upstream-name . "clusterProfiler")))
3825 (build-system r-build-system)
3827 `(("r-annotationdbi" ,r-annotationdbi)
3829 ("r-downloader" ,r-downloader)
3830 ("r-dplyr" ,r-dplyr)
3831 ("r-enrichplot" ,r-enrichplot)
3832 ("r-go-db" ,r-go-db)
3833 ("r-gosemsim" ,r-gosemsim)
3834 ("r-magrittr" ,r-magrittr)
3836 ("r-qvalue" ,r-qvalue)
3837 ("r-rlang" ,r-rlang)
3838 ("r-rvcheck" ,r-rvcheck)
3839 ("r-tidyr" ,r-tidyr)))
3841 `(("r-knitr" ,r-knitr)))
3842 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3843 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3845 "This package implements methods to analyze and visualize functional
3846 profiles (GO and KEGG) of gene and gene clusters.")
3847 (license license:artistic2.0)))
3849 (define-public r-mlinterfaces
3851 (name "r-mlinterfaces")
3856 (uri (bioconductor-uri "MLInterfaces" version))
3859 "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq"))))
3860 (properties `((upstream-name . "MLInterfaces")))
3861 (build-system r-build-system)
3863 `(("r-annotate" ,r-annotate)
3864 ("r-biobase" ,r-biobase)
3865 ("r-biocgenerics" ,r-biocgenerics)
3866 ("r-cluster" ,r-cluster)
3869 ("r-gdata" ,r-gdata)
3870 ("r-genefilter" ,r-genefilter)
3871 ("r-ggvis" ,r-ggvis)
3872 ("r-hwriter" ,r-hwriter)
3874 ("r-mlbench" ,r-mlbench)
3876 ("r-rcolorbrewer" ,r-rcolorbrewer)
3878 ("r-rpart" ,r-rpart)
3879 ("r-sfsmisc" ,r-sfsmisc)
3880 ("r-shiny" ,r-shiny)
3881 ("r-threejs" ,r-threejs)))
3882 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3883 (synopsis "Interfaces to R machine learning procedures")
3885 "This package provides uniform interfaces to machine learning code for
3886 data in R and Bioconductor containers.")
3887 ;; Any version of the LGPL.
3888 (license license:lgpl2.1+)))
3890 (define-public r-annaffy
3897 (uri (bioconductor-uri "annaffy" version))
3900 "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4"))))
3901 (build-system r-build-system)
3904 (modify-phases %standard-phases
3905 (add-after 'unpack 'remove-reference-to-non-free-data
3907 (substitute* "DESCRIPTION"
3911 `(("r-annotationdbi" ,r-annotationdbi)
3912 ("r-biobase" ,r-biobase)
3914 ("r-go-db" ,r-go-db)))
3915 (home-page "https://bioconductor.org/packages/annaffy/")
3916 (synopsis "Annotation tools for Affymetrix biological metadata")
3918 "This package provides functions for handling data from Bioconductor
3919 Affymetrix annotation data packages. It produces compact HTML and text
3920 reports including experimental data and URL links to many online databases.
3921 It allows searching of biological metadata using various criteria.")
3922 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3923 ;; the LGPL 2.1 is included.
3924 (license license:lgpl2.1+)))
3926 (define-public r-a4core
3933 (uri (bioconductor-uri "a4Core" version))
3936 "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp"))))
3937 (properties `((upstream-name . "a4Core")))
3938 (build-system r-build-system)
3940 `(("r-biobase" ,r-biobase)
3941 ("r-glmnet" ,r-glmnet)))
3942 (home-page "https://bioconductor.org/packages/a4Core")
3943 (synopsis "Automated Affymetrix array analysis core package")
3945 "This is the core package for the automated analysis of Affymetrix
3947 (license license:gpl3)))
3949 (define-public r-a4classif
3951 (name "r-a4classif")
3956 (uri (bioconductor-uri "a4Classif" version))
3959 "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr"))))
3960 (properties `((upstream-name . "a4Classif")))
3961 (build-system r-build-system)
3963 `(("r-a4core" ,r-a4core)
3964 ("r-a4preproc" ,r-a4preproc)
3965 ("r-glmnet" ,r-glmnet)
3966 ("r-mlinterfaces" ,r-mlinterfaces)
3969 ("r-varselrf" ,r-varselrf)))
3970 (home-page "https://bioconductor.org/packages/a4Classif/")
3971 (synopsis "Automated Affymetrix array analysis classification package")
3973 "This is the classification package for the automated analysis of
3974 Affymetrix arrays.")
3975 (license license:gpl3)))
3977 (define-public r-a4preproc
3979 (name "r-a4preproc")
3984 (uri (bioconductor-uri "a4Preproc" version))
3987 "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8"))))
3988 (properties `((upstream-name . "a4Preproc")))
3989 (build-system r-build-system)
3991 `(("r-annotationdbi" ,r-annotationdbi)))
3992 (home-page "https://bioconductor.org/packages/a4Preproc/")
3993 (synopsis "Automated Affymetrix array analysis preprocessing package")
3995 "This is a package for the automated analysis of Affymetrix arrays. It
3996 is used for preprocessing the arrays.")
3997 (license license:gpl3)))
3999 (define-public r-a4reporting
4001 (name "r-a4reporting")
4006 (uri (bioconductor-uri "a4Reporting" version))
4009 "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f"))))
4010 (properties `((upstream-name . "a4Reporting")))
4011 (build-system r-build-system)
4013 `(("r-annaffy" ,r-annaffy)
4014 ("r-xtable" ,r-xtable)))
4015 (home-page "https://bioconductor.org/packages/a4Reporting/")
4016 (synopsis "Automated Affymetrix array analysis reporting package")
4018 "This is a package for the automated analysis of Affymetrix arrays. It
4019 provides reporting features.")
4020 (license license:gpl3)))
4022 (define-public r-a4base
4029 (uri (bioconductor-uri "a4Base" version))
4032 "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02"))))
4033 (properties `((upstream-name . "a4Base")))
4034 (build-system r-build-system)
4036 `(("r-a4core" ,r-a4core)
4037 ("r-a4preproc" ,r-a4preproc)
4038 ("r-annaffy" ,r-annaffy)
4039 ("r-annotationdbi" ,r-annotationdbi)
4040 ("r-biobase" ,r-biobase)
4041 ("r-genefilter" ,r-genefilter)
4042 ("r-glmnet" ,r-glmnet)
4043 ("r-gplots" ,r-gplots)
4044 ("r-limma" ,r-limma)
4046 ("r-multtest" ,r-multtest)))
4047 (home-page "https://bioconductor.org/packages/a4Base/")
4048 (synopsis "Automated Affymetrix array analysis base package")
4050 "This package provides basic features for the automated analysis of
4051 Affymetrix arrays.")
4052 (license license:gpl3)))
4061 (uri (bioconductor-uri "a4" version))
4064 "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7"))))
4065 (build-system r-build-system)
4067 `(("r-a4base" ,r-a4base)
4068 ("r-a4classif" ,r-a4classif)
4069 ("r-a4core" ,r-a4core)
4070 ("r-a4preproc" ,r-a4preproc)
4071 ("r-a4reporting" ,r-a4reporting)))
4072 (home-page "https://bioconductor.org/packages/a4/")
4073 (synopsis "Automated Affymetrix array analysis umbrella package")
4075 "This package provides a software suite for the automated analysis of
4076 Affymetrix arrays.")
4077 (license license:gpl3)))
4079 (define-public r-abseqr
4086 (uri (bioconductor-uri "abseqR" version))
4089 "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5"))))
4090 (properties `((upstream-name . "abseqR")))
4091 (build-system r-build-system)
4093 `(("pandoc" ,pandoc)
4094 ("pandoc-citeproc" ,pandoc-citeproc)))
4096 `(("r-biocparallel" ,r-biocparallel)
4097 ("r-biocstyle" ,r-biocstyle)
4098 ("r-circlize" ,r-circlize)
4099 ("r-flexdashboard" ,r-flexdashboard)
4100 ("r-ggcorrplot" ,r-ggcorrplot)
4101 ("r-ggdendro" ,r-ggdendro)
4102 ("r-ggplot2" ,r-ggplot2)
4103 ("r-gridextra" ,r-gridextra)
4104 ("r-knitr" ,r-knitr)
4105 ("r-plotly" ,r-plotly)
4108 ("r-rcolorbrewer" ,r-rcolorbrewer)
4109 ("r-reshape2" ,r-reshape2)
4110 ("r-rmarkdown" ,r-rmarkdown)
4111 ("r-stringr" ,r-stringr)
4112 ("r-vegan" ,r-vegan)
4113 ("r-venndiagram" ,r-venndiagram)))
4115 `(("r-knitr" ,r-knitr)))
4116 (home-page "https://github.com/malhamdoosh/abseqR")
4117 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4119 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4120 sequencing datasets generated from antibody libraries and abseqR is one of its
4121 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4122 capabilities and allows them to generate interactive HTML reports for the
4123 convenience of viewing and sharing with other researchers. Additionally,
4124 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4125 further downstream analysis on its output.")
4126 (license license:gpl3)))
4128 (define-public r-bacon
4135 (uri (bioconductor-uri "bacon" version))
4138 "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl"))))
4139 (build-system r-build-system)
4141 `(("r-biocparallel" ,r-biocparallel)
4142 ("r-ellipse" ,r-ellipse)
4143 ("r-ggplot2" ,r-ggplot2)))
4145 `(("r-knitr" ,r-knitr)))
4146 (home-page "https://bioconductor.org/packages/bacon/")
4147 (synopsis "Controlling bias and inflation in association studies")
4149 "Bacon can be used to remove inflation and bias often observed in
4150 epigenome- and transcriptome-wide association studies. To this end bacon
4151 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4152 fitting a three-component normal mixture on z-scores.")
4153 (license license:gpl2+)))
4155 (define-public r-rgadem
4162 (uri (bioconductor-uri "rGADEM" version))
4165 "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8"))))
4166 (properties `((upstream-name . "rGADEM")))
4167 (build-system r-build-system)
4169 `(("r-biostrings" ,r-biostrings)
4170 ("r-bsgenome" ,r-bsgenome)
4171 ("r-genomicranges" ,r-genomicranges)
4172 ("r-iranges" ,r-iranges)
4173 ("r-seqlogo" ,r-seqlogo)))
4174 (home-page "https://bioconductor.org/packages/rGADEM/")
4175 (synopsis "De novo sequence motif discovery")
4177 "rGADEM is an efficient de novo motif discovery tool for large-scale
4178 genomic sequence data.")
4179 (license license:artistic2.0)))
4181 (define-public r-motiv
4188 (uri (bioconductor-uri "MotIV" version))
4191 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4192 (properties `((upstream-name . "MotIV")))
4193 (build-system r-build-system)
4197 `(("r-biocgenerics" ,r-biocgenerics)
4198 ("r-biostrings" ,r-biostrings)
4199 ("r-genomicranges" ,r-genomicranges)
4200 ("r-iranges" ,r-iranges)
4201 ("r-lattice" ,r-lattice)
4202 ("r-rgadem" ,r-rgadem)
4203 ("r-s4vectors" ,r-s4vectors)))
4204 (home-page "https://bioconductor.org/packages/MotIV/")
4205 (synopsis "Motif identification and validation")
4207 "This package is used for the identification and validation of sequence
4208 motifs. It makes use of STAMP for comparing a set of motifs to a given
4209 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4210 distributions, modules and filter motifs.")
4211 (license license:gpl2)))
4213 (define-public r-motifdb
4219 (uri (bioconductor-uri "MotifDb" version))
4221 (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm"))))
4222 (properties `((upstream-name . "MotifDb")))
4223 (build-system r-build-system)
4225 `(("r-biocgenerics" ,r-biocgenerics)
4226 ("r-biostrings" ,r-biostrings)
4227 ("r-genomicranges" ,r-genomicranges)
4228 ("r-iranges" ,r-iranges)
4229 ("r-rtracklayer" ,r-rtracklayer)
4230 ("r-s4vectors" ,r-s4vectors)
4231 ("r-splitstackshape" ,r-splitstackshape)))
4233 `(("r-knitr" ,r-knitr)))
4234 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4235 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4236 (description "This package provides more than 2000 annotated position
4237 frequency matrices from nine public sources, for multiple organisms.")
4238 (license license:artistic2.0)))
4240 (define-public r-motifbreakr
4242 (name "r-motifbreakr")
4246 (uri (bioconductor-uri "motifbreakR" version))
4248 (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm"))))
4249 (properties `((upstream-name . "motifbreakR")))
4250 (build-system r-build-system)
4252 `(("r-biocgenerics" ,r-biocgenerics)
4253 ("r-biocparallel" ,r-biocparallel)
4254 ("r-biostrings" ,r-biostrings)
4255 ("r-bsgenome" ,r-bsgenome)
4256 ("r-genomeinfodb" ,r-genomeinfodb)
4257 ("r-genomicranges" ,r-genomicranges)
4258 ("r-grimport" ,r-grimport)
4260 ("r-iranges" ,r-iranges)
4261 ("r-matrixstats" ,r-matrixstats)
4262 ("r-motifdb" ,r-motifdb)
4263 ("r-motifstack" ,r-motifstack)
4264 ("r-rtracklayer" ,r-rtracklayer)
4265 ("r-s4vectors" ,r-s4vectors)
4266 ("r-stringr" ,r-stringr)
4267 ("r-summarizedexperiment" ,r-summarizedexperiment)
4268 ("r-tfmpvalue" ,r-tfmpvalue)
4269 ("r-variantannotation" ,r-variantannotation)))
4271 `(("r-knitr" ,r-knitr)))
4272 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4273 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4274 (description "This package allows biologists to judge in the first place
4275 whether the sequence surrounding the polymorphism is a good match, and in
4276 the second place how much information is gained or lost in one allele of
4277 the polymorphism relative to another. This package gives a choice of
4278 algorithms for interrogation of genomes with motifs from public sources:
4280 @item a weighted-sum probability matrix;
4281 @item log-probabilities;
4282 @item weighted by relative entropy.
4285 This package can predict effects for novel or previously described variants in
4286 public databases, making it suitable for tasks beyond the scope of its original
4287 design. Lastly, it can be used to interrogate any genome curated within
4289 (license license:gpl2+)))
4291 (define-public r-motifstack
4293 (name "r-motifstack")
4298 (uri (bioconductor-uri "motifStack" version))
4301 "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd"))))
4302 (properties `((upstream-name . "motifStack")))
4303 (build-system r-build-system)
4305 `(("r-ade4" ,r-ade4)
4306 ("r-biostrings" ,r-biostrings)
4307 ("r-ggplot2" ,r-ggplot2)
4308 ("r-grimport2" ,r-grimport2)
4309 ("r-htmlwidgets" ,r-htmlwidgets)
4310 ("r-motiv" ,r-motiv)
4311 ("r-scales" ,r-scales)
4314 `(("r-knitr" ,r-knitr)))
4315 (home-page "https://bioconductor.org/packages/motifStack/")
4316 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4318 "The motifStack package is designed for graphic representation of
4319 multiple motifs with different similarity scores. It works with both DNA/RNA
4320 sequence motifs and amino acid sequence motifs. In addition, it provides the
4321 flexibility for users to customize the graphic parameters such as the font
4322 type and symbol colors.")
4323 (license license:gpl2+)))
4325 (define-public r-genomicscores
4327 (name "r-genomicscores")
4332 (uri (bioconductor-uri "GenomicScores" version))
4335 "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb"))))
4336 (properties `((upstream-name . "GenomicScores")))
4337 (build-system r-build-system)
4339 `(("r-annotationhub" ,r-annotationhub)
4340 ("r-biobase" ,r-biobase)
4341 ("r-biocgenerics" ,r-biocgenerics)
4342 ("r-biostrings" ,r-biostrings)
4343 ("r-delayedarray" ,r-delayedarray)
4344 ("r-genomeinfodb" ,r-genomeinfodb)
4345 ("r-genomicranges" ,r-genomicranges)
4346 ("r-hdf5array" ,r-hdf5array)
4347 ("r-iranges" ,r-iranges)
4348 ("r-rhdf5" ,r-rhdf5)
4349 ("r-s4vectors" ,r-s4vectors)
4352 `(("r-knitr" ,r-knitr)))
4353 (home-page "https://github.com/rcastelo/GenomicScores/")
4354 (synopsis "Work with genome-wide position-specific scores")
4356 "This package provides infrastructure to store and access genome-wide
4357 position-specific scores within R and Bioconductor.")
4358 (license license:artistic2.0)))
4360 (define-public r-atacseqqc
4362 (name "r-atacseqqc")
4367 (uri (bioconductor-uri "ATACseqQC" version))
4370 "12710c4024pndwwqiiqr6dhrd360z26fc8r3fxhs739gyd0ddk9r"))))
4371 (properties `((upstream-name . "ATACseqQC")))
4372 (build-system r-build-system)
4374 `(("r-biocgenerics" ,r-biocgenerics)
4375 ("r-biostrings" ,r-biostrings)
4376 ("r-bsgenome" ,r-bsgenome)
4377 ("r-chippeakanno" ,r-chippeakanno)
4378 ("r-edger" ,r-edger)
4379 ("r-genomeinfodb" ,r-genomeinfodb)
4380 ("r-genomicalignments" ,r-genomicalignments)
4381 ("r-genomicranges" ,r-genomicranges)
4382 ("r-genomicscores" ,r-genomicscores)
4383 ("r-iranges" ,r-iranges)
4384 ("r-kernsmooth" ,r-kernsmooth)
4385 ("r-limma" ,r-limma)
4386 ("r-motifstack" ,r-motifstack)
4387 ("r-preseqr" ,r-preseqr)
4388 ("r-randomforest" ,r-randomforest)
4389 ("r-rsamtools" ,r-rsamtools)
4390 ("r-rtracklayer" ,r-rtracklayer)
4391 ("r-s4vectors" ,r-s4vectors)))
4393 `(("r-knitr" ,r-knitr)))
4394 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4395 (synopsis "ATAC-seq quality control")
4397 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4398 sequencing, is a rapid and sensitive method for chromatin accessibility
4399 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4400 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4401 assess whether their ATAC-seq experiment is successful. It includes
4402 diagnostic plots of fragment size distribution, proportion of mitochondria
4403 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4405 (license license:gpl2+)))
4407 (define-public r-gofuncr
4414 (uri (bioconductor-uri "GOfuncR" version))
4417 "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1"))))
4418 (properties `((upstream-name . "GOfuncR")))
4419 (build-system r-build-system)
4421 `(("r-annotationdbi" ,r-annotationdbi)
4422 ("r-genomicranges" ,r-genomicranges)
4423 ("r-gtools" ,r-gtools)
4424 ("r-iranges" ,r-iranges)
4425 ("r-mapplots" ,r-mapplots)
4427 ("r-vioplot" ,r-vioplot)))
4429 `(("r-knitr" ,r-knitr)))
4430 (home-page "https://bioconductor.org/packages/GOfuncR/")
4431 (synopsis "Gene ontology enrichment using FUNC")
4433 "GOfuncR performs a gene ontology enrichment analysis based on the
4434 ontology enrichment software FUNC. GO-annotations are obtained from
4435 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4436 included in the package and updated regularly. GOfuncR provides the standard
4437 candidate vs background enrichment analysis using the hypergeometric test, as
4438 well as three additional tests:
4441 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4442 @item a binomial test that is used when genes are associated with two counts,
4444 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4445 associated with four counts.
4448 To correct for multiple testing and interdependency of the tests, family-wise
4449 error rates are computed based on random permutations of the gene-associated
4450 variables. GOfuncR also provides tools for exploring the ontology graph and
4451 the annotations, and options to take gene-length or spatial clustering of
4452 genes into account. It is also possible to provide custom gene coordinates,
4453 annotations and ontologies.")
4454 (license license:gpl2+)))
4456 (define-public r-abaenrichment
4458 (name "r-abaenrichment")
4463 (uri (bioconductor-uri "ABAEnrichment" version))
4466 "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw"))))
4467 (properties `((upstream-name . "ABAEnrichment")))
4468 (build-system r-build-system)
4470 `(("r-abadata" ,r-abadata)
4471 ("r-data-table" ,r-data-table)
4472 ("r-gofuncr" ,r-gofuncr)
4473 ("r-gplots" ,r-gplots)
4474 ("r-gtools" ,r-gtools)
4475 ("r-rcpp" ,r-rcpp)))
4477 `(("r-knitr" ,r-knitr)))
4478 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4479 (synopsis "Gene expression enrichment in human brain regions")
4481 "The package ABAEnrichment is designed to test for enrichment of user
4482 defined candidate genes in the set of expressed genes in different human brain
4483 regions. The core function @code{aba_enrich} integrates the expression of the
4484 candidate gene set (averaged across donors) and the structural information of
4485 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4486 (license license:gpl2+)))
4488 (define-public r-annotationfuncs
4490 (name "r-annotationfuncs")
4495 (uri (bioconductor-uri "AnnotationFuncs" version))
4498 "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d"))))
4500 `((upstream-name . "AnnotationFuncs")))
4501 (build-system r-build-system)
4503 `(("r-annotationdbi" ,r-annotationdbi)
4505 (home-page "https://www.iysik.com/r/annotationfuncs")
4506 (synopsis "Annotation translation functions")
4508 "This package provides functions for handling translating between
4509 different identifieres using the Biocore Data Team data-packages (e.g.
4510 @code{org.Bt.eg.db}).")
4511 (license license:gpl2)))
4513 (define-public r-annotationtools
4515 (name "r-annotationtools")
4520 (uri (bioconductor-uri "annotationTools" version))
4523 "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk"))))
4525 `((upstream-name . "annotationTools")))
4526 (build-system r-build-system)
4527 (propagated-inputs `(("r-biobase" ,r-biobase)))
4528 (home-page "https://bioconductor.org/packages/annotationTools/")
4529 (synopsis "Annotate microarrays and perform gene expression analyses")
4531 "This package provides functions to annotate microarrays, find orthologs,
4532 and integrate heterogeneous gene expression profiles using annotation and
4533 other molecular biology information available as flat file database (plain
4535 ;; Any version of the GPL.
4536 (license (list license:gpl2+))))
4538 (define-public r-allelicimbalance
4540 (name "r-allelicimbalance")
4545 (uri (bioconductor-uri "AllelicImbalance" version))
4548 "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr"))))
4550 `((upstream-name . "AllelicImbalance")))
4551 (build-system r-build-system)
4553 `(("r-annotationdbi" ,r-annotationdbi)
4554 ("r-biocgenerics" ,r-biocgenerics)
4555 ("r-biostrings" ,r-biostrings)
4556 ("r-bsgenome" ,r-bsgenome)
4557 ("r-genomeinfodb" ,r-genomeinfodb)
4558 ("r-genomicalignments" ,r-genomicalignments)
4559 ("r-genomicfeatures" ,r-genomicfeatures)
4560 ("r-genomicranges" ,r-genomicranges)
4561 ("r-gridextra" ,r-gridextra)
4563 ("r-iranges" ,r-iranges)
4564 ("r-lattice" ,r-lattice)
4565 ("r-latticeextra" ,r-latticeextra)
4567 ("r-rsamtools" ,r-rsamtools)
4568 ("r-s4vectors" ,r-s4vectors)
4569 ("r-seqinr" ,r-seqinr)
4570 ("r-summarizedexperiment" ,r-summarizedexperiment)
4571 ("r-variantannotation" ,r-variantannotation)))
4573 `(("r-knitr" ,r-knitr)))
4574 (home-page "https://github.com/pappewaio/AllelicImbalance")
4575 (synopsis "Investigate allele-specific expression")
4577 "This package provides a framework for allele-specific expression
4578 investigation using RNA-seq data.")
4579 (license license:gpl3)))
4581 (define-public r-aucell
4588 (uri (bioconductor-uri "AUCell" version))
4591 "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns"))))
4592 (properties `((upstream-name . "AUCell")))
4593 (build-system r-build-system)
4595 `(("r-biocgenerics" ,r-biocgenerics)
4596 ("r-data-table" ,r-data-table)
4597 ("r-gseabase" ,r-gseabase)
4598 ("r-mixtools" ,r-mixtools)
4599 ("r-r-utils" ,r-r-utils)
4600 ("r-s4vectors" ,r-s4vectors)
4601 ("r-shiny" ,r-shiny)
4602 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4604 `(("r-knitr" ,r-knitr)))
4605 (home-page "https://bioconductor.org/packages/AUCell/")
4606 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4608 "AUCell identifies cells with active gene sets (e.g. signatures,
4609 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4610 Under the Curve} (AUC) to calculate whether a critical subset of the input
4611 gene set is enriched within the expressed genes for each cell. The
4612 distribution of AUC scores across all the cells allows exploring the relative
4613 expression of the signature. Since the scoring method is ranking-based,
4614 AUCell is independent of the gene expression units and the normalization
4615 procedure. In addition, since the cells are evaluated individually, it can
4616 easily be applied to bigger datasets, subsetting the expression matrix if
4618 (license license:gpl3)))
4620 (define-public r-ebimage
4627 (uri (bioconductor-uri "EBImage" version))
4630 "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v"))))
4631 (properties `((upstream-name . "EBImage")))
4632 (build-system r-build-system)
4634 `(("r-abind" ,r-abind)
4635 ("r-biocgenerics" ,r-biocgenerics)
4636 ("r-fftwtools" ,r-fftwtools)
4637 ("r-htmltools" ,r-htmltools)
4638 ("r-htmlwidgets" ,r-htmlwidgets)
4640 ("r-locfit" ,r-locfit)
4642 ("r-rcurl" ,r-rcurl)
4643 ("r-tiff" ,r-tiff)))
4645 `(("r-knitr" ,r-knitr))) ; for vignettes
4646 (home-page "https://github.com/aoles/EBImage")
4647 (synopsis "Image processing and analysis toolbox for R")
4649 "EBImage provides general purpose functionality for image processing and
4650 analysis. In the context of (high-throughput) microscopy-based cellular
4651 assays, EBImage offers tools to segment cells and extract quantitative
4652 cellular descriptors. This allows the automation of such tasks using the R
4653 programming language and facilitates the use of other tools in the R
4654 environment for signal processing, statistical modeling, machine learning and
4655 visualization with image data.")
4656 ;; Any version of the LGPL.
4657 (license license:lgpl2.1+)))
4659 (define-public r-yamss
4666 (uri (bioconductor-uri "yamss" version))
4669 "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c"))))
4670 (build-system r-build-system)
4672 `(("r-biocgenerics" ,r-biocgenerics)
4673 ("r-data-table" ,r-data-table)
4674 ("r-ebimage" ,r-ebimage)
4675 ("r-iranges" ,r-iranges)
4676 ("r-limma" ,r-limma)
4677 ("r-matrix" ,r-matrix)
4679 ("r-s4vectors" ,r-s4vectors)
4680 ("r-summarizedexperiment"
4681 ,r-summarizedexperiment)))
4683 `(("r-knitr" ,r-knitr)))
4684 (home-page "https://github.com/hansenlab/yamss")
4685 (synopsis "Tools for high-throughput metabolomics")
4687 "This package provides tools to analyze and visualize high-throughput
4688 metabolomics data acquired using chromatography-mass spectrometry. These tools
4689 preprocess data in a way that enables reliable and powerful differential
4691 (license license:artistic2.0)))
4693 (define-public r-gtrellis
4700 (uri (bioconductor-uri "gtrellis" version))
4703 "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1"))))
4704 (build-system r-build-system)
4706 `(("r-circlize" ,r-circlize)
4707 ("r-genomicranges" ,r-genomicranges)
4708 ("r-getoptlong" ,r-getoptlong)
4709 ("r-iranges" ,r-iranges)))
4711 `(("r-knitr" ,r-knitr)))
4712 (home-page "https://github.com/jokergoo/gtrellis")
4713 (synopsis "Genome level Trellis layout")
4715 "Genome level Trellis graph visualizes genomic data conditioned by
4716 genomic categories (e.g. chromosomes). For each genomic category, multiple
4717 dimensional data which are represented as tracks describe different features
4718 from different aspects. This package provides high flexibility to arrange
4719 genomic categories and to add self-defined graphics in the plot.")
4720 (license license:expat)))
4722 (define-public r-somaticsignatures
4724 (name "r-somaticsignatures")
4729 (uri (bioconductor-uri "SomaticSignatures" version))
4732 "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1"))))
4734 `((upstream-name . "SomaticSignatures")))
4735 (build-system r-build-system)
4737 `(("r-biobase" ,r-biobase)
4738 ("r-biostrings" ,r-biostrings)
4739 ("r-genomeinfodb" ,r-genomeinfodb)
4740 ("r-genomicranges" ,r-genomicranges)
4741 ("r-ggbio" ,r-ggbio)
4742 ("r-ggplot2" ,r-ggplot2)
4743 ("r-iranges" ,r-iranges)
4745 ("r-pcamethods" ,r-pcamethods)
4746 ("r-proxy" ,r-proxy)
4747 ("r-reshape2" ,r-reshape2)
4748 ("r-s4vectors" ,r-s4vectors)
4749 ("r-variantannotation" ,r-variantannotation)))
4751 `(("r-knitr" ,r-knitr)))
4752 (home-page "https://github.com/juliangehring/SomaticSignatures")
4753 (synopsis "Somatic signatures")
4755 "This package identifies mutational signatures of @dfn{single nucleotide
4756 variants} (SNVs). It provides a infrastructure related to the methodology
4757 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4758 decomposition algorithms.")
4759 (license license:expat)))
4761 (define-public r-yapsa
4768 (uri (bioconductor-uri "YAPSA" version))
4771 "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k"))))
4772 (properties `((upstream-name . "YAPSA")))
4773 (build-system r-build-system)
4775 `(("r-biostrings" ,r-biostrings)
4776 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
4777 ("r-circlize" ,r-circlize)
4778 ("r-complexheatmap" ,r-complexheatmap)
4779 ("r-corrplot" ,r-corrplot)
4780 ("r-dendextend" ,r-dendextend)
4781 ("r-doparallel" ,r-doparallel)
4782 ("r-dplyr" ,r-dplyr)
4783 ("r-genomeinfodb" ,r-genomeinfodb)
4784 ("r-genomicranges" ,r-genomicranges)
4785 ("r-getoptlong" ,r-getoptlong)
4786 ("r-ggbeeswarm" ,r-ggbeeswarm)
4787 ("r-ggplot2" ,r-ggplot2)
4788 ("r-gridextra" ,r-gridextra)
4789 ("r-gtrellis" ,r-gtrellis)
4790 ("r-keggrest" ,r-keggrest)
4792 ("r-magrittr" ,r-magrittr)
4793 ("r-pmcmr" ,r-pmcmr)
4794 ("r-pracma" ,r-pracma)
4795 ("r-reshape2" ,r-reshape2)
4796 ("r-somaticsignatures" ,r-somaticsignatures)
4797 ("r-variantannotation" ,r-variantannotation)))
4799 `(("r-knitr" ,r-knitr)))
4800 (home-page "https://bioconductor.org/packages/YAPSA/")
4801 (synopsis "Yet another package for signature analysis")
4803 "This package provides functions and routines useful in the analysis of
4804 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4805 functions to perform a signature analysis with known signatures and a
4806 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4808 (license license:gpl3)))
4810 (define-public r-gcrma
4817 (uri (bioconductor-uri "gcrma" version))
4820 "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g"))))
4821 (build-system r-build-system)
4823 `(("r-affy" ,r-affy)
4824 ("r-affyio" ,r-affyio)
4825 ("r-biobase" ,r-biobase)
4826 ("r-biocmanager" ,r-biocmanager)
4827 ("r-biostrings" ,r-biostrings)
4828 ("r-xvector" ,r-xvector)))
4829 (home-page "https://bioconductor.org/packages/gcrma/")
4830 (synopsis "Background adjustment using sequence information")
4832 "Gcrma adjusts for background intensities in Affymetrix array data which
4833 include optical noise and @dfn{non-specific binding} (NSB). The main function
4834 @code{gcrma} converts background adjusted probe intensities to expression
4835 measures using the same normalization and summarization methods as a
4836 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4837 to estimate probe affinity to NSB. The sequence information is summarized in
4838 a more complex way than the simple GC content. Instead, the base types (A, T,
4839 G or C) at each position along the probe determine the affinity of each probe.
4840 The parameters of the position-specific base contributions to the probe
4841 affinity is estimated in an NSB experiment in which only NSB but no
4842 gene-specific bidning is expected.")
4843 ;; Any version of the LGPL
4844 (license license:lgpl2.1+)))
4846 (define-public r-simpleaffy
4848 (name "r-simpleaffy")
4853 (uri (bioconductor-uri "simpleaffy" version))
4856 "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7"))))
4857 (build-system r-build-system)
4859 `(("r-affy" ,r-affy)
4860 ("r-biobase" ,r-biobase)
4861 ("r-biocgenerics" ,r-biocgenerics)
4862 ("r-gcrma" ,r-gcrma)
4863 ("r-genefilter" ,r-genefilter)))
4864 (home-page "https://bioconductor.org/packages/simpleaffy/")
4865 (synopsis "Very simple high level analysis of Affymetrix data")
4867 "This package provides high level functions for reading Affy @file{.CEL}
4868 files, phenotypic data, and then computing simple things with it, such as
4869 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4870 library. It also has some basic scatter plot functions and mechanisms for
4871 generating high resolution journal figures.")
4872 (license license:gpl2+)))
4874 (define-public r-yaqcaffy
4881 (uri (bioconductor-uri "yaqcaffy" version))
4884 "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0"))))
4885 (build-system r-build-system)
4887 `(("r-simpleaffy" ,r-simpleaffy)))
4888 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4889 (synopsis "Affymetrix quality control and reproducibility analysis")
4891 "This is a package that can be used for quality control of Affymetrix
4892 GeneChip expression data and reproducibility analysis of human whole genome
4893 chips with the MAQC reference datasets.")
4894 (license license:artistic2.0)))
4896 (define-public r-quantro
4903 (uri (bioconductor-uri "quantro" version))
4906 "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz"))))
4907 (build-system r-build-system)
4909 `(("r-biobase" ,r-biobase)
4910 ("r-doparallel" ,r-doparallel)
4911 ("r-foreach" ,r-foreach)
4912 ("r-ggplot2" ,r-ggplot2)
4913 ("r-iterators" ,r-iterators)
4914 ("r-minfi" ,r-minfi)
4915 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4917 `(("r-knitr" ,r-knitr)))
4918 (home-page "https://bioconductor.org/packages/quantro/")
4919 (synopsis "Test for when to use quantile normalization")
4921 "This package provides a data-driven test for the assumptions of quantile
4922 normalization using raw data such as objects that inherit eSets (e.g.
4923 ExpressionSet, MethylSet). Group level information about each sample (such as
4924 Tumor / Normal status) must also be provided because the test assesses if
4925 there are global differences in the distributions between the user-defined
4927 (license license:gpl3+)))
4929 (define-public r-yarn
4936 (uri (bioconductor-uri "yarn" version))
4939 "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx"))))
4940 (build-system r-build-system)
4942 `(("r-biobase" ,r-biobase)
4943 ("r-biomart" ,r-biomart)
4944 ("r-downloader" ,r-downloader)
4945 ("r-edger" ,r-edger)
4946 ("r-gplots" ,r-gplots)
4947 ("r-limma" ,r-limma)
4948 ("r-matrixstats" ,r-matrixstats)
4949 ("r-preprocesscore" ,r-preprocesscore)
4950 ("r-quantro" ,r-quantro)
4951 ("r-rcolorbrewer" ,r-rcolorbrewer)
4952 ("r-readr" ,r-readr)))
4954 `(("r-knitr" ,r-knitr)))
4955 (home-page "https://bioconductor.org/packages/yarn/")
4956 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4958 "Expedite large RNA-Seq analyses using a combination of previously
4959 developed tools. YARN is meant to make it easier for the user in performing
4960 basic mis-annotation quality control, filtering, and condition-aware
4961 normalization. YARN leverages many Bioconductor tools and statistical
4962 techniques to account for the large heterogeneity and sparsity found in very
4963 large RNA-seq experiments.")
4964 (license license:artistic2.0)))
4966 (define-public r-roar
4973 (uri (bioconductor-uri "roar" version))
4976 "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f"))))
4977 (build-system r-build-system)
4979 `(("r-biocgenerics" ,r-biocgenerics)
4980 ("r-genomeinfodb" ,r-genomeinfodb)
4981 ("r-genomicalignments" ,r-genomicalignments)
4982 ("r-genomicranges" ,r-genomicranges)
4983 ("r-iranges" ,r-iranges)
4984 ("r-rtracklayer" ,r-rtracklayer)
4985 ("r-s4vectors" ,r-s4vectors)
4986 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4987 (home-page "https://github.com/vodkatad/roar/")
4988 (synopsis "Identify differential APA usage from RNA-seq alignments")
4990 "This package provides tools for identifying preferential usage of APA
4991 sites, comparing two biological conditions, starting from known alternative
4992 sites and alignments obtained from standard RNA-seq experiments.")
4993 (license license:gpl3)))
4995 (define-public r-xbseq
5002 (uri (bioconductor-uri "XBSeq" version))
5005 "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0"))))
5006 (properties `((upstream-name . "XBSeq")))
5007 (build-system r-build-system)
5009 `(("r-biobase" ,r-biobase)
5010 ("r-deseq2" ,r-deseq2)
5011 ("r-dplyr" ,r-dplyr)
5012 ("r-ggplot2" ,r-ggplot2)
5013 ("r-locfit" ,r-locfit)
5014 ("r-magrittr" ,r-magrittr)
5015 ("r-matrixstats" ,r-matrixstats)
5016 ("r-pracma" ,r-pracma)
5017 ("r-roar" ,r-roar)))
5019 `(("r-knitr" ,r-knitr)))
5020 (home-page "https://github.com/Liuy12/XBSeq")
5021 (synopsis "Test for differential expression for RNA-seq data")
5023 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5024 expression} (DE), where a statistical model was established based on the
5025 assumption that observed signals are the convolution of true expression
5026 signals and sequencing noises. The mapped reads in non-exonic regions are
5027 considered as sequencing noises, which follows a Poisson distribution. Given
5028 measurable observed signal and background noise from RNA-seq data, true
5029 expression signals, assuming governed by the negative binomial distribution,
5030 can be delineated and thus the accurate detection of differential expressed
5032 (license license:gpl3+)))
5034 (define-public r-massspecwavelet
5036 (name "r-massspecwavelet")
5041 (uri (bioconductor-uri "MassSpecWavelet" version))
5044 "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq"))))
5046 `((upstream-name . "MassSpecWavelet")))
5047 (build-system r-build-system)
5049 `(("r-waveslim" ,r-waveslim)))
5050 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5051 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5053 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5054 data mainly through the use of wavelet transforms. It supports peak detection
5055 based on @dfn{Continuous Wavelet Transform} (CWT).")
5056 (license license:lgpl2.0+)))
5058 (define-public r-xcms
5065 (uri (bioconductor-uri "xcms" version))
5068 "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn"))))
5069 (build-system r-build-system)
5071 `(("r-biobase" ,r-biobase)
5072 ("r-biocgenerics" ,r-biocgenerics)
5073 ("r-biocparallel" ,r-biocparallel)
5074 ("r-iranges" ,r-iranges)
5075 ("r-lattice" ,r-lattice)
5076 ("r-massspecwavelet" ,r-massspecwavelet)
5077 ("r-msnbase" ,r-msnbase)
5080 ("r-protgenerics" ,r-protgenerics)
5082 ("r-rcolorbrewer" ,r-rcolorbrewer)
5083 ("r-robustbase" ,r-robustbase)
5084 ("r-s4vectors" ,r-s4vectors)
5085 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5087 `(("r-knitr" ,r-knitr)))
5088 (home-page "https://bioconductor.org/packages/xcms/")
5089 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5091 "This package provides a framework for processing and visualization of
5092 chromatographically separated and single-spectra mass spectral data. It
5093 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5094 data for high-throughput, untargeted analyte profiling.")
5095 (license license:gpl2+)))
5097 (define-public r-wrench
5104 (uri (bioconductor-uri "Wrench" version))
5107 "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6"))))
5108 (properties `((upstream-name . "Wrench")))
5109 (build-system r-build-system)
5111 `(("r-limma" ,r-limma)
5112 ("r-locfit" ,r-locfit)
5113 ("r-matrixstats" ,r-matrixstats)))
5115 `(("r-knitr" ,r-knitr)))
5116 (home-page "https://github.com/HCBravoLab/Wrench")
5117 (synopsis "Wrench normalization for sparse count data")
5119 "Wrench is a package for normalization sparse genomic count data, like
5120 that arising from 16s metagenomic surveys.")
5121 (license license:artistic2.0)))
5123 (define-public r-wiggleplotr
5125 (name "r-wiggleplotr")
5130 (uri (bioconductor-uri "wiggleplotr" version))
5133 "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp"))))
5134 (build-system r-build-system)
5136 `(("r-assertthat" ,r-assertthat)
5137 ("r-cowplot" ,r-cowplot)
5138 ("r-dplyr" ,r-dplyr)
5139 ("r-genomeinfodb" ,r-genomeinfodb)
5140 ("r-genomicranges" ,r-genomicranges)
5141 ("r-ggplot2" ,r-ggplot2)
5142 ("r-iranges" ,r-iranges)
5143 ("r-purrr" ,r-purrr)
5144 ("r-rtracklayer" ,r-rtracklayer)
5145 ("r-s4vectors" ,r-s4vectors)))
5147 `(("r-knitr" ,r-knitr)))
5148 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5149 (synopsis "Make read coverage plots from BigWig files")
5151 "This package provides tools to visualize read coverage from sequencing
5152 experiments together with genomic annotations (genes, transcripts, peaks).
5153 Introns of long transcripts can be rescaled to a fixed length for better
5154 visualization of exonic read coverage.")
5155 (license license:asl2.0)))
5157 (define-public r-widgettools
5159 (name "r-widgettools")
5164 (uri (bioconductor-uri "widgetTools" version))
5167 "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx"))))
5168 (properties `((upstream-name . "widgetTools")))
5169 (build-system r-build-system)
5170 (home-page "https://bioconductor.org/packages/widgetTools/")
5171 (synopsis "Tools for creating interactive tcltk widgets")
5173 "This package contains tools to support the construction of tcltk
5175 ;; Any version of the LGPL.
5176 (license license:lgpl3+)))
5178 (define-public r-webbioc
5185 (uri (bioconductor-uri "webbioc" version))
5188 "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f"))))
5189 (build-system r-build-system)
5191 `(("netpbm" ,netpbm)
5194 `(("r-affy" ,r-affy)
5195 ("r-annaffy" ,r-annaffy)
5196 ("r-biobase" ,r-biobase)
5197 ("r-biocmanager" ,r-biocmanager)
5198 ("r-gcrma" ,r-gcrma)
5199 ("r-multtest" ,r-multtest)
5200 ("r-qvalue" ,r-qvalue)
5202 (home-page "https://www.bioconductor.org/")
5203 (synopsis "Bioconductor web interface")
5205 "This package provides an integrated web interface for doing microarray
5206 analysis using several of the Bioconductor packages. It is intended to be
5207 deployed as a centralized bioinformatics resource for use by many users.
5208 Currently only Affymetrix oligonucleotide analysis is supported.")
5209 (license license:gpl2+)))
5211 (define-public r-zfpkm
5218 (uri (bioconductor-uri "zFPKM" version))
5221 "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys"))))
5222 (properties `((upstream-name . "zFPKM")))
5223 (build-system r-build-system)
5225 `(("r-checkmate" ,r-checkmate)
5226 ("r-dplyr" ,r-dplyr)
5227 ("r-ggplot2" ,r-ggplot2)
5228 ("r-summarizedexperiment" ,r-summarizedexperiment)
5229 ("r-tidyr" ,r-tidyr)))
5231 `(("r-knitr" ,r-knitr)))
5232 (home-page "https://github.com/ronammar/zFPKM/")
5233 (synopsis "Functions to facilitate zFPKM transformations")
5235 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5236 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5238 (license license:gpl3)))
5240 (define-public r-rbowtie2
5247 (uri (bioconductor-uri "Rbowtie2" version))
5250 "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7"))))
5251 (properties `((upstream-name . "Rbowtie2")))
5252 (build-system r-build-system)
5256 `(("r-knitr" ,r-knitr)))
5257 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5258 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5260 "This package provides an R wrapper of the popular @code{bowtie2}
5261 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5262 rapid adapter trimming, identification, and read merging.")
5263 (license license:gpl3+)))
5265 (define-public r-progeny
5272 (uri (bioconductor-uri "progeny" version))
5275 "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh"))))
5276 (build-system r-build-system)
5278 `(("r-biobase" ,r-biobase)
5279 ("r-dplyr" ,r-dplyr)
5280 ("r-ggplot2" ,r-ggplot2)
5281 ("r-ggrepel" ,r-ggrepel)
5282 ("r-gridextra" ,r-gridextra)
5283 ("r-tidyr" ,r-tidyr)))
5285 `(("r-knitr" ,r-knitr)))
5286 (home-page "https://github.com/saezlab/progeny")
5287 (synopsis "Pathway responsive gene activity inference")
5289 "This package provides a function to infer pathway activity from gene
5290 expression. It contains the linear model inferred in the publication
5291 \"Perturbation-response genes reveal signaling footprints in cancer gene
5293 (license license:asl2.0)))
5295 (define-public r-arrmnormalization
5297 (name "r-arrmnormalization")
5302 (uri (bioconductor-uri "ARRmNormalization" version))
5305 "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv"))))
5307 `((upstream-name . "ARRmNormalization")))
5308 (build-system r-build-system)
5309 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5310 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5311 (synopsis "Adaptive robust regression normalization for methylation data")
5313 "This is a package to perform the @dfn{Adaptive Robust Regression
5314 method} (ARRm) for the normalization of methylation data from the Illumina
5315 Infinium HumanMethylation 450k assay.")
5316 (license license:artistic2.0)))
5318 (define-public r-biocfilecache
5320 (name "r-biocfilecache")
5325 (uri (bioconductor-uri "BiocFileCache" version))
5328 "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf"))))
5329 (properties `((upstream-name . "BiocFileCache")))
5330 (build-system r-build-system)
5332 `(("r-curl" ,r-curl)
5334 ("r-dbplyr" ,r-dbplyr)
5335 ("r-dplyr" ,r-dplyr)
5337 ("r-rappdirs" ,r-rappdirs)
5338 ("r-rsqlite" ,r-rsqlite)))
5340 `(("r-knitr" ,r-knitr)))
5341 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5342 (synopsis "Manage files across sessions")
5344 "This package creates a persistent on-disk cache of files that the user
5345 can add, update, and retrieve. It is useful for managing resources (such as
5346 custom Txdb objects) that are costly or difficult to create, web resources,
5347 and data files used across sessions.")
5348 (license license:artistic2.0)))
5350 (define-public r-iclusterplus
5352 (name "r-iclusterplus")
5357 (uri (bioconductor-uri "iClusterPlus" version))
5360 "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w"))))
5361 (properties `((upstream-name . "iClusterPlus")))
5362 (build-system r-build-system)
5363 (native-inputs `(("gfortran" ,gfortran)))
5364 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5365 (synopsis "Integrative clustering of multi-type genomic data")
5367 "iClusterPlus is developed for integrative clustering analysis of
5368 multi-type genomic data and is an enhanced version of iCluster proposed and
5369 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5370 from the experiments where biological samples (e.g. tumor samples) are
5371 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5372 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5373 on. In the iClusterPlus model, binary observations such as somatic mutation
5374 are modeled as Binomial processes; categorical observations such as copy
5375 number states are realizations of Multinomial random variables; counts are
5376 modeled as Poisson random processes; and continuous measures are modeled by
5377 Gaussian distributions.")
5378 (license license:gpl2+)))
5380 (define-public r-rbowtie
5387 (uri (bioconductor-uri "Rbowtie" version))
5390 "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3"))))
5391 (properties `((upstream-name . "Rbowtie")))
5392 (build-system r-build-system)
5396 `(("r-knitr" ,r-knitr)))
5397 (home-page "https://bioconductor.org/packages/Rbowtie/")
5398 (synopsis "R bowtie wrapper")
5400 "This package provides an R wrapper around the popular bowtie short read
5401 aligner and around SpliceMap, a de novo splice junction discovery and
5403 (license license:artistic2.0)))
5405 (define-public r-sgseq
5412 (uri (bioconductor-uri "SGSeq" version))
5415 "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c"))))
5416 (properties `((upstream-name . "SGSeq")))
5417 (build-system r-build-system)
5419 `(("r-annotationdbi" ,r-annotationdbi)
5420 ("r-biocgenerics" ,r-biocgenerics)
5421 ("r-biostrings" ,r-biostrings)
5422 ("r-genomeinfodb" ,r-genomeinfodb)
5423 ("r-genomicalignments" ,r-genomicalignments)
5424 ("r-genomicfeatures" ,r-genomicfeatures)
5425 ("r-genomicranges" ,r-genomicranges)
5426 ("r-igraph" ,r-igraph)
5427 ("r-iranges" ,r-iranges)
5428 ("r-rsamtools" ,r-rsamtools)
5429 ("r-rtracklayer" ,r-rtracklayer)
5430 ("r-runit" ,r-runit)
5431 ("r-s4vectors" ,r-s4vectors)
5432 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5434 `(("r-knitr" ,r-knitr)))
5435 (home-page "https://bioconductor.org/packages/SGSeq/")
5436 (synopsis "Splice event prediction and quantification from RNA-seq data")
5438 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5439 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5440 represented as a splice graph, which can be obtained from existing annotation
5441 or predicted from the mapped sequence reads. Splice events are identified
5442 from the graph and are quantified locally using structurally compatible reads
5443 at the start or end of each splice variant. The software includes functions
5444 for splice event prediction, quantification, visualization and
5446 (license license:artistic2.0)))
5448 (define-public r-rhisat2
5455 (uri (bioconductor-uri "Rhisat2" version))
5458 "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a"))))
5459 (properties `((upstream-name . "Rhisat2")))
5460 (build-system r-build-system)
5463 (modify-phases %standard-phases
5464 (add-after 'unpack 'make-reproducible
5466 (substitute* "src/Makefile"
5467 (("`hostname`") "guix")
5469 ;; Avoid shelling out to "which".
5470 (("^CC =.*") (which "gcc"))
5471 (("^CPP =.*") (which "g++")))
5474 `(("r-genomicfeatures" ,r-genomicfeatures)
5475 ("r-genomicranges" ,r-genomicranges)
5476 ("r-sgseq" ,r-sgseq)))
5478 `(("r-knitr" ,r-knitr)))
5479 (home-page "https://github.com/fmicompbio/Rhisat2")
5480 (synopsis "R Wrapper for HISAT2 sequence aligner")
5482 "This package provides an R interface to the HISAT2 spliced short-read
5483 aligner by Kim et al. (2015). The package contains wrapper functions to
5484 create a genome index and to perform the read alignment to the generated
5486 (license license:gpl3)))
5488 (define-public r-quasr
5495 (uri (bioconductor-uri "QuasR" version))
5498 "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8"))))
5499 (properties `((upstream-name . "QuasR")))
5500 (build-system r-build-system)
5504 `(("r-annotationdbi" ,r-annotationdbi)
5505 ("r-biobase" ,r-biobase)
5506 ("r-biocgenerics" ,r-biocgenerics)
5507 ("r-biocmanager" ,r-biocmanager)
5508 ("r-biocparallel" ,r-biocparallel)
5509 ("r-biostrings" ,r-biostrings)
5510 ("r-bsgenome" ,r-bsgenome)
5511 ("r-genomeinfodb" ,r-genomeinfodb)
5512 ("r-genomicalignments" ,r-genomicalignments)
5513 ("r-genomicfeatures" ,r-genomicfeatures)
5514 ("r-genomicfiles" ,r-genomicfiles)
5515 ("r-genomicranges" ,r-genomicranges)
5516 ("r-iranges" ,r-iranges)
5517 ("r-rbowtie" ,r-rbowtie)
5518 ("r-rhisat2" ,r-rhisat2)
5519 ("r-rhtslib" ,r-rhtslib)
5520 ("r-rsamtools" ,r-rsamtools)
5521 ("r-rtracklayer" ,r-rtracklayer)
5522 ("r-s4vectors" ,r-s4vectors)
5523 ("r-shortread" ,r-shortread)))
5525 `(("r-knitr" ,r-knitr)))
5526 (home-page "https://bioconductor.org/packages/QuasR/")
5527 (synopsis "Quantify and annotate short reads in R")
5529 "This package provides a framework for the quantification and analysis of
5530 short genomic reads. It covers a complete workflow starting from raw sequence
5531 reads, over creation of alignments and quality control plots, to the
5532 quantification of genomic regions of interest.")
5533 (license license:gpl2)))
5535 (define-public r-rqc
5542 (uri (bioconductor-uri "Rqc" version))
5545 "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3"))))
5546 (properties `((upstream-name . "Rqc")))
5547 (build-system r-build-system)
5549 `(("r-biocgenerics" ,r-biocgenerics)
5550 ("r-biocparallel" ,r-biocparallel)
5551 ("r-biocstyle" ,r-biocstyle)
5552 ("r-biostrings" ,r-biostrings)
5553 ("r-biovizbase" ,r-biovizbase)
5554 ("r-genomicalignments" ,r-genomicalignments)
5555 ("r-genomicfiles" ,r-genomicfiles)
5556 ("r-ggplot2" ,r-ggplot2)
5557 ("r-iranges" ,r-iranges)
5558 ("r-knitr" ,r-knitr)
5559 ("r-markdown" ,r-markdown)
5562 ("r-reshape2" ,r-reshape2)
5563 ("r-rsamtools" ,r-rsamtools)
5564 ("r-s4vectors" ,r-s4vectors)
5565 ("r-shiny" ,r-shiny)
5566 ("r-shortread" ,r-shortread)))
5568 `(("r-knitr" ,r-knitr)))
5569 (home-page "https://github.com/labbcb/Rqc")
5570 (synopsis "Quality control tool for high-throughput sequencing data")
5572 "Rqc is an optimized tool designed for quality control and assessment of
5573 high-throughput sequencing data. It performs parallel processing of entire
5574 files and produces a report which contains a set of high-resolution
5576 (license license:gpl2+)))
5578 (define-public r-birewire
5585 (uri (bioconductor-uri "BiRewire" version))
5588 "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g"))))
5589 (properties `((upstream-name . "BiRewire")))
5590 (build-system r-build-system)
5592 `(("r-igraph" ,r-igraph)
5593 ("r-matrix" ,r-matrix)
5595 ("r-tsne" ,r-tsne)))
5596 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5597 (synopsis "Tools for randomization of bipartite graphs")
5599 "This package provides functions for bipartite network rewiring through N
5600 consecutive switching steps and for the computation of the minimal number of
5601 switching steps to be performed in order to maximise the dissimilarity with
5602 respect to the original network. It includes functions for the analysis of
5603 the introduced randomness across the switching steps and several other
5604 routines to analyse the resulting networks and their natural projections.")
5605 (license license:gpl3)))
5607 (define-public r-birta
5614 (uri (bioconductor-uri "birta" version))
5617 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
5618 (build-system r-build-system)
5620 `(("r-biobase" ,r-biobase)
5621 ("r-limma" ,r-limma)
5622 ("r-mass" ,r-mass)))
5623 (home-page "https://bioconductor.org/packages/birta")
5624 (synopsis "Bayesian inference of regulation of transcriptional activity")
5626 "Expression levels of mRNA molecules are regulated by different
5627 processes, comprising inhibition or activation by transcription factors and
5628 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5629 Inference of Regulation of Transcriptional Activity) uses the regulatory
5630 networks of transcription factors and miRNAs together with mRNA and miRNA
5631 expression data to predict switches in regulatory activity between two
5632 conditions. A Bayesian network is used to model the regulatory structure and
5633 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5634 (license license:gpl2+)))
5636 (define-public r-multidataset
5638 (name "r-multidataset")
5643 (uri (bioconductor-uri "MultiDataSet" version))
5646 "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39"))))
5647 (properties `((upstream-name . "MultiDataSet")))
5648 (build-system r-build-system)
5650 `(("r-biobase" ,r-biobase)
5651 ("r-biocgenerics" ,r-biocgenerics)
5652 ("r-genomicranges" ,r-genomicranges)
5653 ("r-ggplot2" ,r-ggplot2)
5654 ("r-ggrepel" ,r-ggrepel)
5655 ("r-iranges" ,r-iranges)
5656 ("r-limma" ,r-limma)
5657 ("r-qqman" ,r-qqman)
5658 ("r-s4vectors" ,r-s4vectors)
5659 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5661 `(("r-knitr" ,r-knitr)))
5662 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5663 (synopsis "Implementation of MultiDataSet and ResultSet")
5665 "This package provides an implementation of the BRGE's (Bioinformatic
5666 Research Group in Epidemiology from Center for Research in Environmental
5667 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5668 integrating multi omics data sets and ResultSet is a container for omics
5669 results. This package contains base classes for MEAL and rexposome
5671 (license license:expat)))
5673 (define-public r-ropls
5680 (uri (bioconductor-uri "ropls" version))
5683 "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx"))))
5684 (build-system r-build-system)
5686 `(("r-biobase" ,r-biobase)
5687 ("r-multidataset" ,r-multidataset)))
5689 `(("r-knitr" ,r-knitr))) ; for vignettes
5690 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5691 (synopsis "Multivariate analysis and feature selection of omics data")
5693 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5694 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5695 regression, classification, and feature selection of omics data where the
5696 number of variables exceeds the number of samples and with multicollinearity
5697 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5698 separately model the variation correlated (predictive) to the factor of
5699 interest and the uncorrelated (orthogonal) variation. While performing
5700 similarly to PLS, OPLS facilitates interpretation.
5702 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5703 analysis and feature selection of omics data. In addition to scores, loadings
5704 and weights plots, the package provides metrics and graphics to determine the
5705 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5706 validity of the model by permutation testing, detect outliers, and perform
5707 feature selection (e.g. with Variable Importance in Projection or regression
5709 (license license:cecill)))
5711 (define-public r-biosigner
5713 (name "r-biosigner")
5718 (uri (bioconductor-uri "biosigner" version))
5721 "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06"))))
5722 (build-system r-build-system)
5724 `(("r-biobase" ,r-biobase)
5725 ("r-e1071" ,r-e1071)
5726 ("r-multidataset" ,r-multidataset)
5727 ("r-randomforest" ,r-randomforest)
5728 ("r-ropls" ,r-ropls)))
5730 `(("r-knitr" ,r-knitr)))
5731 (home-page "https://bioconductor.org/packages/biosigner/")
5732 (synopsis "Signature discovery from omics data")
5734 "Feature selection is critical in omics data analysis to extract
5735 restricted and meaningful molecular signatures from complex and high-dimension
5736 data, and to build robust classifiers. This package implements a method to
5737 assess the relevance of the variables for the prediction performances of the
5738 classifier. The approach can be run in parallel with the PLS-DA, Random
5739 Forest, and SVM binary classifiers. The signatures and the corresponding
5740 'restricted' models are returned, enabling future predictions on new
5742 (license license:cecill)))
5744 (define-public r-annotatr
5751 (uri (bioconductor-uri "annotatr" version))
5754 "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl"))))
5755 (build-system r-build-system)
5757 `(("r-annotationdbi" ,r-annotationdbi)
5758 ("r-annotationhub" ,r-annotationhub)
5759 ("r-dplyr" ,r-dplyr)
5760 ("r-genomeinfodb" ,r-genomeinfodb)
5761 ("r-genomicfeatures" ,r-genomicfeatures)
5762 ("r-genomicranges" ,r-genomicranges)
5763 ("r-ggplot2" ,r-ggplot2)
5764 ("r-iranges" ,r-iranges)
5765 ("r-readr" ,r-readr)
5766 ("r-regioner" ,r-regioner)
5767 ("r-reshape2" ,r-reshape2)
5768 ("r-rtracklayer" ,r-rtracklayer)
5769 ("r-s4vectors" ,r-s4vectors)))
5771 `(("r-knitr" ,r-knitr)))
5772 (home-page "https://bioconductor.org/packages/annotatr/")
5773 (synopsis "Annotation of genomic regions to genomic annotations")
5775 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5776 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5777 to investigate the intersecting genomic annotations. Such annotations include
5778 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5779 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5780 enhancers. The annotatr package provides an easy way to summarize and
5781 visualize the intersection of genomic sites/regions with genomic
5783 (license license:gpl3)))
5785 (define-public r-rsubread
5792 (uri (bioconductor-uri "Rsubread" version))
5795 "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm"))))
5796 (properties `((upstream-name . "Rsubread")))
5797 (build-system r-build-system)
5798 (inputs `(("zlib" ,zlib)))
5800 `(("r-matrix" ,r-matrix)))
5801 (home-page "https://bioconductor.org/packages/Rsubread/")
5802 (synopsis "Subread sequence alignment and counting for R")
5804 "This package provides tools for alignment, quantification and analysis
5805 of second and third generation sequencing data. It includes functionality for
5806 read mapping, read counting, SNP calling, structural variant detection and
5807 gene fusion discovery. It can be applied to all major sequencing techologies
5808 and to both short and long sequence reads.")
5809 (license license:gpl3)))
5811 (define-public r-flowutils
5813 (name "r-flowutils")
5818 (uri (bioconductor-uri "flowUtils" version))
5821 "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4"))))
5822 (properties `((upstream-name . "flowUtils")))
5823 (build-system r-build-system)
5825 `(("r-biobase" ,r-biobase)
5826 ("r-corpcor" ,r-corpcor)
5827 ("r-flowcore" ,r-flowcore)
5828 ("r-graph" ,r-graph)
5829 ("r-runit" ,r-runit)
5831 (home-page "https://github.com/jspidlen/flowUtils")
5832 (synopsis "Utilities for flow cytometry")
5834 "This package provides utilities for flow cytometry data.")
5835 (license license:artistic2.0)))
5837 (define-public r-consensusclusterplus
5839 (name "r-consensusclusterplus")
5844 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5847 "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq"))))
5849 `((upstream-name . "ConsensusClusterPlus")))
5850 (build-system r-build-system)
5853 ("r-biobase" ,r-biobase)
5854 ("r-cluster" ,r-cluster)))
5855 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5856 (synopsis "Clustering algorithm")
5858 "This package provides an implementation of an algorithm for determining
5859 cluster count and membership by stability evidence in unsupervised analysis.")
5860 (license license:gpl2)))
5862 (define-public r-cytolib
5869 (uri (bioconductor-uri "cytolib" version))
5872 "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj"))))
5873 (properties `((upstream-name . "cytolib")))
5874 (build-system r-build-system)
5878 `(("r-knitr" ,r-knitr)))
5882 ("r-rcpparmadillo" ,r-rcpparmadillo)
5883 ("r-rcppparallel" ,r-rcppparallel)
5884 ("r-rhdf5lib" ,r-rhdf5lib)
5885 ("r-rprotobuflib" ,r-rprotobuflib)))
5886 (home-page "https://bioconductor.org/packages/cytolib/")
5887 (synopsis "C++ infrastructure for working with gated cytometry")
5889 "This package provides the core data structure and API to represent and
5890 interact with gated cytometry data.")
5891 (license license:artistic2.0)))
5893 (define-public r-flowcore
5900 (uri (bioconductor-uri "flowCore" version))
5903 "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p"))))
5904 (properties `((upstream-name . "flowCore")))
5905 (build-system r-build-system)
5908 ("r-biobase" ,r-biobase)
5909 ("r-biocgenerics" ,r-biocgenerics)
5910 ("r-cytolib" ,r-cytolib)
5911 ("r-matrixstats" ,r-matrixstats)
5913 ("r-rcpparmadillo" ,r-rcpparmadillo)
5914 ("r-rprotobuflib" ,r-rprotobuflib)))
5916 `(("r-knitr" ,r-knitr)))
5917 (home-page "https://bioconductor.org/packages/flowCore")
5918 (synopsis "Basic structures for flow cytometry data")
5920 "This package provides S4 data structures and basic functions to deal
5921 with flow cytometry data.")
5922 (license license:artistic2.0)))
5924 (define-public r-flowmeans
5926 (name "r-flowmeans")
5931 (uri (bioconductor-uri "flowMeans" version))
5934 "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7"))))
5935 (properties `((upstream-name . "flowMeans")))
5936 (build-system r-build-system)
5938 `(("r-biobase" ,r-biobase)
5939 ("r-feature" ,r-feature)
5940 ("r-flowcore" ,r-flowcore)
5941 ("r-rrcov" ,r-rrcov)))
5942 (home-page "https://bioconductor.org/packages/flowMeans")
5943 (synopsis "Non-parametric flow cytometry data gating")
5945 "This package provides tools to identify cell populations in Flow
5946 Cytometry data using non-parametric clustering and segmented-regression-based
5947 change point detection.")
5948 (license license:artistic2.0)))
5950 (define-public r-ncdfflow
5957 (uri (bioconductor-uri "ncdfFlow" version))
5960 "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f"))))
5961 (properties `((upstream-name . "ncdfFlow")))
5962 (build-system r-build-system)
5967 ("r-biobase" ,r-biobase)
5968 ("r-biocgenerics" ,r-biocgenerics)
5969 ("r-flowcore" ,r-flowcore)
5971 ("r-rcpparmadillo" ,r-rcpparmadillo)
5972 ("r-rhdf5lib" ,r-rhdf5lib)
5973 ("r-zlibbioc" ,r-zlibbioc)))
5975 `(("r-knitr" ,r-knitr)))
5976 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5977 (synopsis "HDF5 based storage for flow cytometry data")
5979 "This package provides HDF5 storage based methods and functions for
5980 manipulation of flow cytometry data.")
5981 (license license:artistic2.0)))
5983 (define-public r-ggcyto
5990 (uri (bioconductor-uri "ggcyto" version))
5993 "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0"))))
5994 (properties `((upstream-name . "ggcyto")))
5995 (build-system r-build-system)
5997 `(("r-data-table" ,r-data-table)
5998 ("r-flowcore" ,r-flowcore)
5999 ("r-flowworkspace" ,r-flowworkspace)
6000 ("r-ggplot2" ,r-ggplot2)
6001 ("r-gridextra" ,r-gridextra)
6002 ("r-hexbin" ,r-hexbin)
6003 ("r-ncdfflow" ,r-ncdfflow)
6005 ("r-rcolorbrewer" ,r-rcolorbrewer)
6006 ("r-rlang" ,r-rlang)
6007 ("r-scales" ,r-scales)))
6009 `(("r-knitr" ,r-knitr)))
6010 (home-page "https://github.com/RGLab/ggcyto/issues")
6011 (synopsis "Visualize Cytometry data with ggplot")
6013 "With the dedicated fortify method implemented for @code{flowSet},
6014 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6015 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6016 and some custom layers also make it easy to add gates and population
6017 statistics to the plot.")
6018 (license license:artistic2.0)))
6020 (define-public r-flowviz
6027 (uri (bioconductor-uri "flowViz" version))
6030 "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq"))))
6031 (properties `((upstream-name . "flowViz")))
6032 (build-system r-build-system)
6034 `(("r-biobase" ,r-biobase)
6035 ("r-flowcore" ,r-flowcore)
6036 ("r-hexbin" ,r-hexbin)
6037 ("r-idpmisc" ,r-idpmisc)
6038 ("r-kernsmooth" ,r-kernsmooth)
6039 ("r-lattice" ,r-lattice)
6040 ("r-latticeextra" ,r-latticeextra)
6042 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6044 `(("r-knitr" ,r-knitr)))
6045 (home-page "https://bioconductor.org/packages/flowViz/")
6046 (synopsis "Visualization for flow cytometry")
6048 "This package provides visualization tools for flow cytometry data.")
6049 (license license:artistic2.0)))
6051 (define-public r-flowclust
6053 (name "r-flowclust")
6058 (uri (bioconductor-uri "flowClust" version))
6061 "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b"))))
6062 (properties `((upstream-name . "flowClust")))
6063 (build-system r-build-system)
6066 (list "--configure-args=--enable-bundled-gsl=no")))
6068 `(("r-biobase" ,r-biobase)
6069 ("r-biocgenerics" ,r-biocgenerics)
6071 ("r-corpcor" ,r-corpcor)
6072 ("r-ellipse" ,r-ellipse)
6073 ("r-flowcore" ,r-flowcore)
6074 ("r-flowviz" ,r-flowviz)
6075 ("r-graph" ,r-graph)
6076 ("r-mnormt" ,r-mnormt)))
6080 `(("pkg-config" ,pkg-config)
6081 ("r-knitr" ,r-knitr)))
6082 (home-page "https://bioconductor.org/packages/flowClust")
6083 (synopsis "Clustering for flow cytometry")
6085 "This package provides robust model-based clustering using a t-mixture
6086 model with Box-Cox transformation.")
6087 (license license:artistic2.0)))
6089 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6090 ;; make it use our protobuf package instead.
6091 (define-public r-rprotobuflib
6093 (name "r-rprotobuflib")
6098 (uri (bioconductor-uri "RProtoBufLib" version))
6101 "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps"))))
6102 (properties `((upstream-name . "RProtoBufLib")))
6103 (build-system r-build-system)
6106 (modify-phases %standard-phases
6107 (add-after 'unpack 'unpack-bundled-sources
6109 (with-directory-excursion "src"
6110 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6113 `(("r-knitr" ,r-knitr)))
6114 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6115 (synopsis "C++ headers and static libraries of Protocol buffers")
6117 "This package provides the headers and static library of Protocol buffers
6118 for other R packages to compile and link against.")
6119 (license license:bsd-3)))
6121 (define-public r-flowworkspace
6123 (name "r-flowworkspace")
6128 (uri (bioconductor-uri "flowWorkspace" version))
6131 "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v"))))
6132 (properties `((upstream-name . "flowWorkspace")))
6133 (build-system r-build-system)
6136 ("r-biobase" ,r-biobase)
6137 ("r-biocgenerics" ,r-biocgenerics)
6138 ("r-cytolib" ,r-cytolib)
6139 ("r-data-table" ,r-data-table)
6140 ("r-digest" ,r-digest)
6141 ("r-dplyr" ,r-dplyr)
6142 ("r-flowcore" ,r-flowcore)
6143 ("r-ggplot2" ,r-ggplot2)
6144 ("r-graph" ,r-graph)
6145 ("r-lattice" ,r-lattice)
6146 ("r-latticeextra" ,r-latticeextra)
6147 ("r-matrixstats" ,r-matrixstats)
6148 ("r-ncdfflow" ,r-ncdfflow)
6151 ("r-rcpparmadillo" ,r-rcpparmadillo)
6152 ("r-rcppparallel" ,r-rcppparallel)
6153 ("r-rgraphviz" ,r-rgraphviz)
6154 ("r-rhdf5lib" ,r-rhdf5lib)
6155 ("r-rprotobuflib" ,r-rprotobuflib)
6156 ("r-scales" ,r-scales)
6157 ("r-stringr" ,r-stringr)
6160 `(("r-knitr" ,r-knitr)))
6161 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6162 (synopsis "Infrastructure for working with cytometry data")
6164 "This package is designed to facilitate comparison of automated gating
6165 methods against manual gating done in flowJo. This package allows you to
6166 import basic flowJo workspaces into BioConductor and replicate the gating from
6167 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6168 samples, compensation, and transformation are performed so that the output
6169 matches the flowJo analysis.")
6170 (license license:artistic2.0)))
6172 (define-public r-flowstats
6174 (name "r-flowstats")
6179 (uri (bioconductor-uri "flowStats" version))
6182 "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir"))))
6183 (properties `((upstream-name . "flowStats")))
6184 (build-system r-build-system)
6186 `(("r-biobase" ,r-biobase)
6187 ("r-biocgenerics" ,r-biocgenerics)
6188 ("r-cluster" ,r-cluster)
6190 ("r-flowcore" ,r-flowcore)
6191 ("r-flowviz" ,r-flowviz)
6192 ("r-flowworkspace" ,r-flowworkspace)
6193 ("r-kernsmooth" ,r-kernsmooth)
6195 ("r-lattice" ,r-lattice)
6197 ("r-ncdfflow" ,r-ncdfflow)
6198 ("r-rcolorbrewer" ,r-rcolorbrewer)
6199 ("r-rrcov" ,r-rrcov)))
6200 (home-page "http://www.github.com/RGLab/flowStats")
6201 (synopsis "Statistical methods for the analysis of flow cytometry data")
6203 "This package provides methods and functionality to analyze flow data
6204 that is beyond the basic infrastructure provided by the @code{flowCore}
6206 (license license:artistic2.0)))
6208 (define-public r-opencyto
6215 (uri (bioconductor-uri "openCyto" version))
6218 "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m"))))
6219 (properties `((upstream-name . "openCyto")))
6220 (build-system r-build-system)
6222 `(("r-biobase" ,r-biobase)
6223 ("r-biocgenerics" ,r-biocgenerics)
6225 ("r-data-table" ,r-data-table)
6226 ("r-flowclust" ,r-flowclust)
6227 ("r-flowcore" ,r-flowcore)
6228 ("r-flowstats" ,r-flowstats)
6229 ("r-flowviz" ,r-flowviz)
6230 ("r-flowworkspace" ,r-flowworkspace)
6231 ("r-graph" ,r-graph)
6232 ("r-gtools" ,r-gtools)
6234 ("r-lattice" ,r-lattice)
6236 ("r-ncdfflow" ,r-ncdfflow)
6238 ("r-r-utils" ,r-r-utils)
6240 ("r-rcolorbrewer" ,r-rcolorbrewer)
6242 ("r-rrcov" ,r-rrcov)))
6244 `(("r-knitr" ,r-knitr)))
6245 (home-page "https://bioconductor.org/packages/openCyto")
6246 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6248 "This package is designed to facilitate the automated gating methods in a
6249 sequential way to mimic the manual gating strategy.")
6250 (license license:artistic2.0)))
6252 (define-public r-cytoml
6259 (uri (bioconductor-uri "CytoML" version))
6262 "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n"))))
6263 (properties `((upstream-name . "CytoML")))
6264 (build-system r-build-system)
6266 `(("libxml2" ,libxml2)))
6268 `(("r-base64enc" ,r-base64enc)
6270 ("r-biobase" ,r-biobase)
6271 ("r-corpcor" ,r-corpcor)
6272 ("r-cytolib" ,r-cytolib)
6273 ("r-data-table" ,r-data-table)
6274 ("r-dplyr" ,r-dplyr)
6275 ("r-flowcore" ,r-flowcore)
6276 ("r-flowworkspace" ,r-flowworkspace)
6277 ("r-ggcyto" ,r-ggcyto)
6278 ("r-graph" ,r-graph)
6279 ("r-jsonlite" ,r-jsonlite)
6280 ("r-lattice" ,r-lattice)
6281 ("r-opencyto" ,r-opencyto)
6285 ("r-rcpparmadillo" ,r-rcpparmadillo)
6286 ("r-rcppparallel" ,r-rcppparallel)
6287 ("r-rgraphviz" ,r-rgraphviz)
6288 ("r-rhdf5lib" ,r-rhdf5lib)
6289 ("r-rprotobuflib" ,r-rprotobuflib)
6290 ("r-runit" ,r-runit)
6291 ("r-tibble" ,r-tibble)
6294 ("r-yaml" ,r-yaml)))
6296 `(("r-knitr" ,r-knitr)))
6297 (home-page "https://github.com/RGLab/CytoML")
6298 (synopsis "GatingML interface for cross platform cytometry data sharing")
6300 "This package provides an interface to implementations of the GatingML2.0
6301 standard to exchange gated cytometry data with other software platforms.")
6302 (license license:artistic2.0)))
6304 (define-public r-flowsom
6311 (uri (bioconductor-uri "FlowSOM" version))
6314 "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78"))))
6315 (properties `((upstream-name . "FlowSOM")))
6316 (build-system r-build-system)
6318 `(("r-biocgenerics" ,r-biocgenerics)
6319 ("r-consensusclusterplus" ,r-consensusclusterplus)
6320 ("r-cytoml" ,r-cytoml)
6321 ("r-flowcore" ,r-flowcore)
6322 ("r-flowworkspace" ,r-flowworkspace)
6323 ("r-igraph" ,r-igraph)
6324 ("r-rcolorbrewer" ,r-rcolorbrewer)
6327 (home-page "https://bioconductor.org/packages/FlowSOM/")
6328 (synopsis "Visualize and interpret cytometry data")
6330 "FlowSOM offers visualization options for cytometry data, by using
6331 self-organizing map clustering and minimal spanning trees.")
6332 (license license:gpl2+)))
6334 (define-public r-mixomics
6341 (uri (bioconductor-uri "mixOmics" version))
6344 "13kq9l5xwhwp30y5gfqfh5f11n63vn8rk195mb2y2mww4cwi6lv4"))))
6345 (properties `((upstream-name . "mixOmics")))
6346 (build-system r-build-system)
6348 `(("r-corpcor" ,r-corpcor)
6349 ("r-dplyr" ,r-dplyr)
6350 ("r-ellipse" ,r-ellipse)
6351 ("r-ggplot2" ,r-ggplot2)
6352 ("r-gridextra" ,r-gridextra)
6353 ("r-igraph" ,r-igraph)
6354 ("r-lattice" ,r-lattice)
6356 ("r-matrixstats" ,r-matrixstats)
6357 ("r-rarpack" ,r-rarpack)
6358 ("r-rcolorbrewer" ,r-rcolorbrewer)
6359 ("r-reshape2" ,r-reshape2)
6360 ("r-tidyr" ,r-tidyr)))
6362 `(("r-knitr" ,r-knitr)))
6363 (home-page "http://www.mixOmics.org")
6364 (synopsis "Multivariate methods for exploration of biological datasets")
6366 "mixOmics offers a wide range of multivariate methods for the exploration
6367 and integration of biological datasets with a particular focus on variable
6368 selection. The package proposes several sparse multivariate models we have
6369 developed to identify the key variables that are highly correlated, and/or
6370 explain the biological outcome of interest. The data that can be analysed
6371 with mixOmics may come from high throughput sequencing technologies, such as
6372 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6373 also beyond the realm of omics (e.g. spectral imaging). The methods
6374 implemented in mixOmics can also handle missing values without having to
6375 delete entire rows with missing data.")
6376 (license license:gpl2+)))
6378 (define-public r-depecher
6385 (uri (bioconductor-uri "DepecheR" version))
6388 "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
6389 (properties `((upstream-name . "DepecheR")))
6390 (build-system r-build-system)
6392 `(("r-beanplot" ,r-beanplot)
6393 ("r-dosnow" ,r-dosnow)
6394 ("r-dplyr" ,r-dplyr)
6396 ("r-foreach" ,r-foreach)
6397 ("r-ggplot2" ,r-ggplot2)
6398 ("r-gplots" ,r-gplots)
6400 ("r-matrixstats" ,r-matrixstats)
6401 ("r-mixomics" ,r-mixomics)
6402 ("r-moments" ,r-moments)
6404 ("r-rcppeigen" ,r-rcppeigen)
6405 ("r-reshape2" ,r-reshape2)
6406 ("r-robustbase" ,r-robustbase)
6407 ("r-viridis" ,r-viridis)))
6409 `(("r-knitr" ,r-knitr)))
6410 (home-page "https://bioconductor.org/packages/DepecheR/")
6411 (synopsis "Identify traits of clusters in high-dimensional entities")
6413 "The purpose of this package is to identify traits in a dataset that can
6414 separate groups. This is done on two levels. First, clustering is performed,
6415 using an implementation of sparse K-means. Secondly, the generated clusters
6416 are used to predict outcomes of groups of individuals based on their
6417 distribution of observations in the different clusters. As certain clusters
6418 with separating information will be identified, and these clusters are defined
6419 by a sparse number of variables, this method can reduce the complexity of
6420 data, to only emphasize the data that actually matters.")
6421 (license license:expat)))
6423 (define-public r-rcistarget
6425 (name "r-rcistarget")
6430 (uri (bioconductor-uri "RcisTarget" version))
6433 "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i"))))
6434 (properties `((upstream-name . "RcisTarget")))
6435 (build-system r-build-system)
6437 `(("r-aucell" ,r-aucell)
6438 ("r-biocgenerics" ,r-biocgenerics)
6439 ("r-data-table" ,r-data-table)
6440 ("r-feather" ,r-feather)
6441 ("r-gseabase" ,r-gseabase)
6442 ("r-r-utils" ,r-r-utils)
6443 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6445 `(("r-knitr" ,r-knitr)))
6446 (home-page "https://aertslab.org/#scenic")
6447 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6449 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6450 over-represented on a gene list. In a first step, RcisTarget selects DNA
6451 motifs that are significantly over-represented in the surroundings of the
6452 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6453 achieved by using a database that contains genome-wide cross-species rankings
6454 for each motif. The motifs that are then annotated to TFs and those that have
6455 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6456 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6457 genes in the gene-set that are ranked above the leading edge).")
6458 (license license:gpl3)))
6460 (define-public r-cicero
6467 (uri (bioconductor-uri "cicero" version))
6470 "0nf9yqg5krj26n4n82iyx3rsr84d46b17i9zfk35sh12l4xssbii"))))
6471 (build-system r-build-system)
6473 `(("r-assertthat" ,r-assertthat)
6474 ("r-biobase" ,r-biobase)
6475 ("r-biocgenerics" ,r-biocgenerics)
6476 ("r-data-table" ,r-data-table)
6477 ("r-dplyr" ,r-dplyr)
6479 ("r-genomicranges" ,r-genomicranges)
6480 ("r-ggplot2" ,r-ggplot2)
6481 ("r-glasso" ,r-glasso)
6483 ("r-igraph" ,r-igraph)
6484 ("r-iranges" ,r-iranges)
6485 ("r-matrix" ,r-matrix)
6486 ("r-monocle" ,r-monocle)
6488 ("r-reshape2" ,r-reshape2)
6489 ("r-s4vectors" ,r-s4vectors)
6490 ("r-stringi" ,r-stringi)
6491 ("r-stringr" ,r-stringr)
6492 ("r-tibble" ,r-tibble)
6493 ("r-tidyr" ,r-tidyr)
6494 ("r-vgam" ,r-vgam)))
6496 `(("r-knitr" ,r-knitr)))
6497 (home-page "https://bioconductor.org/packages/cicero/")
6498 (synopsis "Predict cis-co-accessibility from single-cell data")
6500 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6501 accessibility data. It also extends the monocle package for use in chromatin
6502 accessibility data.")
6503 (license license:expat)))
6505 ;; This is the latest commit on the "monocle3" branch.
6506 (define-public r-cicero-monocle3
6507 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6509 (package (inherit r-cicero)
6510 (name "r-cicero-monocle3")
6511 (version (git-version "1.3.2" revision commit))
6516 (url "https://github.com/cole-trapnell-lab/cicero-release")
6518 (file-name (git-file-name name version))
6521 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6523 `(("r-monocle3" ,r-monocle3)
6524 ,@(alist-delete "r-monocle"
6525 (package-propagated-inputs r-cicero)))))))
6527 (define-public r-cistopic
6528 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6532 (version (git-version "0.2.1" revision commit))
6537 (url "https://github.com/aertslab/cisTopic")
6539 (file-name (git-file-name name version))
6542 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6543 (build-system r-build-system)
6545 `(("r-aucell" ,r-aucell)
6546 ("r-data-table" ,r-data-table)
6547 ("r-dplyr" ,r-dplyr)
6548 ("r-dosnow" ,r-dosnow)
6550 ("r-feather" ,r-feather)
6551 ("r-fitdistrplus" ,r-fitdistrplus)
6552 ("r-genomicranges" ,r-genomicranges)
6553 ("r-ggplot2" ,r-ggplot2)
6555 ("r-matrix" ,r-matrix)
6557 ("r-rcistarget" ,r-rcistarget)
6558 ("r-rtracklayer" ,r-rtracklayer)
6559 ("r-s4vectors" ,r-s4vectors)))
6560 (home-page "https://github.com/aertslab/cisTopic")
6561 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6563 "The sparse nature of single cell epigenomics data can be overruled using
6564 probabilistic modelling methods such as @dfn{Latent Dirichlet
6565 Allocation} (LDA). This package allows the probabilistic modelling of
6566 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6567 includes functionalities to identify cell states based on the contribution of
6568 cisTopics and explore the nature and regulatory proteins driving them.")
6569 (license license:gpl3))))
6571 (define-public r-genie3
6578 (uri (bioconductor-uri "GENIE3" version))
6581 "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7"))))
6582 (properties `((upstream-name . "GENIE3")))
6583 (build-system r-build-system)
6584 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6586 `(("r-knitr" ,r-knitr)))
6587 (home-page "https://bioconductor.org/packages/GENIE3")
6588 (synopsis "Gene network inference with ensemble of trees")
6590 "This package implements the GENIE3 algorithm for inferring gene
6591 regulatory networks from expression data.")
6592 (license license:gpl2+)))
6594 (define-public r-roc
6601 (uri (bioconductor-uri "ROC" version))
6604 "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89"))))
6605 (properties `((upstream-name . "ROC")))
6606 (build-system r-build-system)
6608 `(("r-knitr" ,r-knitr)))
6609 (home-page "https://www.bioconductor.org/packages/ROC/")
6610 (synopsis "Utilities for ROC curves")
6612 "This package provides utilities for @dfn{Receiver Operating
6613 Characteristic} (ROC) curves, with a focus on micro arrays.")
6614 (license license:artistic2.0)))
6616 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6618 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6623 (uri (bioconductor-uri
6624 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6625 version 'annotation))
6628 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6631 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6632 (build-system r-build-system)
6633 (propagated-inputs `(("r-minfi" ,r-minfi)))
6635 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6636 (synopsis "Annotation for Illumina's 450k methylation arrays")
6638 "This package provides manifests and annotation for Illumina's 450k array
6640 (license license:artistic2.0)))
6642 (define-public r-watermelon
6644 (name "r-watermelon")
6649 (uri (bioconductor-uri "wateRmelon" version))
6652 "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn"))))
6653 (properties `((upstream-name . "wateRmelon")))
6654 (build-system r-build-system)
6656 `(("r-biobase" ,r-biobase)
6657 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6658 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6659 ("r-illuminaio" ,r-illuminaio)
6660 ("r-limma" ,r-limma)
6662 ("r-matrixstats" ,r-matrixstats)
6663 ("r-methylumi" ,r-methylumi)
6665 (home-page "https://bioconductor.org/packages/wateRmelon/")
6666 (synopsis "Illumina 450 methylation array normalization and metrics")
6668 "The standard index of DNA methylation (beta) is computed from methylated
6669 and unmethylated signal intensities. Betas calculated from raw signal
6670 intensities perform well, but using 11 methylomic datasets we demonstrate that
6671 quantile normalization methods produce marked improvement. The commonly used
6672 procedure of normalizing betas is inferior to the separate normalization of M
6673 and U, and it is also advantageous to normalize Type I and Type II assays
6674 separately. This package provides 15 flavours of betas and three performance
6675 metrics, with methods for objects produced by the @code{methylumi} and
6676 @code{minfi} packages.")
6677 (license license:gpl3)))
6679 (define-public r-gdsfmt
6686 (uri (bioconductor-uri "gdsfmt" version))
6689 "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67"))
6690 (modules '((guix build utils)))
6691 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6692 ;; them and link with system libraries instead.
6695 (for-each delete-file-recursively
6699 (substitute* "src/Makevars"
6700 (("all: \\$\\(SHLIB\\)") "all:")
6701 (("\\$\\(SHLIB\\): liblzma.a") "")
6702 (("(ZLIB|LZ4)/.*") "")
6703 (("CoreArray/dVLIntGDS.cpp.*")
6704 "CoreArray/dVLIntGDS.cpp")
6705 (("CoreArray/dVLIntGDS.o.*")
6706 "CoreArray/dVLIntGDS.o")
6707 (("PKG_LIBS = ./liblzma.a")
6708 "PKG_LIBS = -llz4"))
6709 (substitute* "src/CoreArray/dStream.h"
6710 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6711 (string-append "include <" header ">")))
6713 (properties `((upstream-name . "gdsfmt")))
6714 (build-system r-build-system)
6720 `(("r-knitr" ,r-knitr)))
6721 (home-page "http://corearray.sourceforge.net/")
6723 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6725 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6726 Data Structure} (GDS) data files, which are portable across platforms with
6727 hierarchical structure to store multiple scalable array-oriented data sets
6728 with metadata information. It is suited for large-scale datasets, especially
6729 for data which are much larger than the available random-access memory. The
6730 @code{gdsfmt} package offers efficient operations specifically designed for
6731 integers of less than 8 bits, since a diploid genotype, like
6732 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6733 byte. Data compression and decompression are available with relatively
6734 efficient random access. It is also allowed to read a GDS file in parallel
6735 with multiple R processes supported by the package @code{parallel}.")
6736 (license license:lgpl3)))
6738 (define-public r-bigmelon
6745 (uri (bioconductor-uri "bigmelon" version))
6748 "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y"))))
6749 (properties `((upstream-name . "bigmelon")))
6750 (build-system r-build-system)
6752 `(("r-biobase" ,r-biobase)
6753 ("r-biocgenerics" ,r-biocgenerics)
6754 ("r-gdsfmt" ,r-gdsfmt)
6755 ("r-geoquery" ,r-geoquery)
6756 ("r-methylumi" ,r-methylumi)
6757 ("r-minfi" ,r-minfi)
6758 ("r-watermelon" ,r-watermelon)))
6759 (home-page "https://bioconductor.org/packages/bigmelon/")
6760 (synopsis "Illumina methylation array analysis for large experiments")
6762 "This package provides methods for working with Illumina arrays using the
6763 @code{gdsfmt} package.")
6764 (license license:gpl3)))
6766 (define-public r-seqbias
6773 (uri (bioconductor-uri "seqbias" version))
6776 "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai"))))
6777 (properties `((upstream-name . "seqbias")))
6778 (build-system r-build-system)
6780 `(("r-biostrings" ,r-biostrings)
6781 ("r-genomicranges" ,r-genomicranges)
6782 ("r-rhtslib" ,r-rhtslib)))
6784 `(("zlib" ,zlib))) ; This comes from rhtslib.
6785 (home-page "https://bioconductor.org/packages/seqbias/")
6786 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6788 "This package implements a model of per-position sequencing bias in
6789 high-throughput sequencing data using a simple Bayesian network, the structure
6790 and parameters of which are trained on a set of aligned reads and a reference
6792 (license license:lgpl3)))
6794 (define-public r-snplocs-hsapiens-dbsnp144-grch37
6796 (name "r-snplocs-hsapiens-dbsnp144-grch37")
6800 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
6801 version 'annotation))
6804 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
6805 (build-system r-build-system)
6806 ;; As this package provides little more than a very large data file it
6807 ;; doesn't make sense to build substitutes.
6808 (arguments `(#:substitutable? #f))
6810 `(("r-biocgenerics" ,r-biocgenerics)
6811 ("r-s4vectors" ,r-s4vectors)
6812 ("r-iranges" ,r-iranges)
6813 ("r-genomeinfodb" ,r-genomeinfodb)
6814 ("r-genomicranges" ,r-genomicranges)
6815 ("r-bsgenome" ,r-bsgenome)
6816 ("r-biostrings" ,r-biostrings)))
6818 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
6819 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
6820 (description "This package provides SNP locations and alleles for Homo
6821 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
6822 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
6823 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
6824 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
6825 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
6826 the mitochondrion chromosome. Therefore, the SNPs in this package can be
6827 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
6828 correct position but this injection will exclude chrM (i.e. nothing will be
6829 injected in that sequence).")
6830 (license license:artistic2.0)))
6832 (define-public r-reqon
6839 (uri (bioconductor-uri "ReQON" version))
6842 "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz"))))
6843 (properties `((upstream-name . "ReQON")))
6844 (build-system r-build-system)
6846 `(("r-rjava" ,r-rjava)
6847 ("r-rsamtools" ,r-rsamtools)
6848 ("r-seqbias" ,r-seqbias)))
6849 (home-page "https://bioconductor.org/packages/ReQON/")
6850 (synopsis "Recalibrating quality of nucleotides")
6852 "This package provides an implementation of an algorithm for
6853 recalibrating the base quality scores for aligned sequencing data in BAM
6855 (license license:gpl2)))
6857 (define-public r-wavcluster
6859 (name "r-wavcluster")
6864 (uri (bioconductor-uri "wavClusteR" version))
6867 "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk"))))
6868 (properties `((upstream-name . "wavClusteR")))
6869 (build-system r-build-system)
6871 `(("r-biocgenerics" ,r-biocgenerics)
6872 ("r-biostrings" ,r-biostrings)
6873 ("r-foreach" ,r-foreach)
6874 ("r-genomicfeatures" ,r-genomicfeatures)
6875 ("r-genomicranges" ,r-genomicranges)
6876 ("r-ggplot2" ,r-ggplot2)
6877 ("r-hmisc" ,r-hmisc)
6878 ("r-iranges" ,r-iranges)
6879 ("r-mclust" ,r-mclust)
6880 ("r-rsamtools" ,r-rsamtools)
6881 ("r-rtracklayer" ,r-rtracklayer)
6882 ("r-s4vectors" ,r-s4vectors)
6883 ("r-seqinr" ,r-seqinr)
6884 ("r-stringr" ,r-stringr)
6885 ("r-wmtsa" ,r-wmtsa)))
6887 `(("r-knitr" ,r-knitr)))
6888 (home-page "https://bioconductor.org/packages/wavClusteR/")
6889 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6891 "This package provides an integrated pipeline for the analysis of
6892 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6893 sequencing errors, SNPs and additional non-experimental sources by a non-
6894 parametric mixture model. The protein binding sites (clusters) are then
6895 resolved at high resolution and cluster statistics are estimated using a
6896 rigorous Bayesian framework. Post-processing of the results, data export for
6897 UCSC genome browser visualization and motif search analysis are provided. In
6898 addition, the package integrates RNA-Seq data to estimate the False
6899 Discovery Rate of cluster detection. Key functions support parallel multicore
6900 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6901 be applied to the analysis of other NGS data obtained from experimental
6902 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6903 (license license:gpl2)))
6905 (define-public r-timeseriesexperiment
6907 (name "r-timeseriesexperiment")
6912 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6915 "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3"))))
6917 `((upstream-name . "TimeSeriesExperiment")))
6918 (build-system r-build-system)
6920 `(("r-deseq2" ,r-deseq2)
6921 ("r-dplyr" ,r-dplyr)
6922 ("r-dynamictreecut" ,r-dynamictreecut)
6923 ("r-edger" ,r-edger)
6924 ("r-ggplot2" ,r-ggplot2)
6925 ("r-hmisc" ,r-hmisc)
6926 ("r-limma" ,r-limma)
6927 ("r-magrittr" ,r-magrittr)
6928 ("r-proxy" ,r-proxy)
6929 ("r-s4vectors" ,r-s4vectors)
6930 ("r-summarizedexperiment" ,r-summarizedexperiment)
6931 ("r-tibble" ,r-tibble)
6932 ("r-tidyr" ,r-tidyr)
6933 ("r-vegan" ,r-vegan)
6934 ("r-viridis" ,r-viridis)))
6936 `(("r-knitr" ,r-knitr)))
6937 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6938 (synopsis "Analysis for short time-series data")
6940 "This package is a visualization and analysis toolbox for short time
6941 course data which includes dimensionality reduction, clustering, two-sample
6942 differential expression testing and gene ranking techniques. The package also
6943 provides methods for retrieving enriched pathways.")
6944 (license license:lgpl3+)))
6946 (define-public r-variantfiltering
6948 (name "r-variantfiltering")
6953 (uri (bioconductor-uri "VariantFiltering" version))
6956 "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4"))))
6958 `((upstream-name . "VariantFiltering")))
6959 (build-system r-build-system)
6961 `(("r-annotationdbi" ,r-annotationdbi)
6962 ("r-biobase" ,r-biobase)
6963 ("r-biocgenerics" ,r-biocgenerics)
6964 ("r-biocparallel" ,r-biocparallel)
6965 ("r-biostrings" ,r-biostrings)
6966 ("r-bsgenome" ,r-bsgenome)
6968 ("r-genomeinfodb" ,r-genomeinfodb)
6969 ("r-genomicfeatures" ,r-genomicfeatures)
6970 ("r-genomicranges" ,r-genomicranges)
6971 ("r-genomicscores" ,r-genomicscores)
6972 ("r-graph" ,r-graph)
6974 ("r-iranges" ,r-iranges)
6976 ("r-rsamtools" ,r-rsamtools)
6977 ("r-s4vectors" ,r-s4vectors)
6978 ("r-shiny" ,r-shiny)
6979 ("r-shinyjs" ,r-shinyjs)
6980 ("r-shinythemes" ,r-shinythemes)
6981 ("r-shinytree" ,r-shinytree)
6982 ("r-summarizedexperiment" ,r-summarizedexperiment)
6983 ("r-variantannotation" ,r-variantannotation)
6984 ("r-xvector" ,r-xvector)))
6985 (home-page "https://github.com/rcastelo/VariantFiltering")
6986 (synopsis "Filtering of coding and non-coding genetic variants")
6988 "Filter genetic variants using different criteria such as inheritance
6989 model, amino acid change consequence, minor allele frequencies across human
6990 populations, splice site strength, conservation, etc.")
6991 (license license:artistic2.0)))
6993 (define-public r-genomegraphs
6995 (name "r-genomegraphs")
7000 (uri (bioconductor-uri "GenomeGraphs" version))
7003 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7004 (properties `((upstream-name . "GenomeGraphs")))
7005 (build-system r-build-system)
7007 `(("r-biomart" ,r-biomart)))
7008 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7009 (synopsis "Plotting genomic information from Ensembl")
7011 "Genomic data analyses requires integrated visualization of known genomic
7012 information and new experimental data. GenomeGraphs uses the biomaRt package
7013 to perform live annotation queries to Ensembl and translates this to e.g.
7014 gene/transcript structures in viewports of the grid graphics package. This
7015 results in genomic information plotted together with your data. Another
7016 strength of GenomeGraphs is to plot different data types such as array CGH,
7017 gene expression, sequencing and other data, together in one plot using the
7018 same genome coordinate system.")
7019 (license license:artistic2.0)))
7021 (define-public r-wavetiling
7023 (name "r-wavetiling")
7028 (uri (bioconductor-uri "waveTiling" version))
7031 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7032 (properties `((upstream-name . "waveTiling")))
7033 (build-system r-build-system)
7035 `(("r-affy" ,r-affy)
7036 ("r-biobase" ,r-biobase)
7037 ("r-biostrings" ,r-biostrings)
7038 ("r-genomegraphs" ,r-genomegraphs)
7039 ("r-genomicranges" ,r-genomicranges)
7040 ("r-iranges" ,r-iranges)
7041 ("r-oligo" ,r-oligo)
7042 ("r-oligoclasses" ,r-oligoclasses)
7043 ("r-preprocesscore" ,r-preprocesscore)
7044 ("r-waveslim" ,r-waveslim)))
7045 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7046 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7048 "This package is designed to conduct transcriptome analysis for tiling
7049 arrays based on fast wavelet-based functional models.")
7050 (license license:gpl2+)))
7052 (define-public r-variancepartition
7054 (name "r-variancepartition")
7059 (uri (bioconductor-uri "variancePartition" version))
7062 "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0"))))
7064 `((upstream-name . "variancePartition")))
7065 (build-system r-build-system)
7067 `(("r-biobase" ,r-biobase)
7068 ("r-biocparallel" ,r-biocparallel)
7069 ("r-colorramps" ,r-colorramps)
7070 ("r-doparallel" ,r-doparallel)
7071 ("r-foreach" ,r-foreach)
7072 ("r-ggplot2" ,r-ggplot2)
7073 ("r-gplots" ,r-gplots)
7074 ("r-iterators" ,r-iterators)
7075 ("r-limma" ,r-limma)
7077 ("r-lmertest" ,r-lmertest)
7079 ("r-pbkrtest" ,r-pbkrtest)
7080 ("r-progress" ,r-progress)
7081 ("r-reshape2" ,r-reshape2)
7082 ("r-scales" ,r-scales)))
7084 `(("r-knitr" ,r-knitr)))
7085 (home-page "https://bioconductor.org/packages/variancePartition/")
7086 (synopsis "Analyze variation in gene expression experiments")
7088 "This is a package providing tools to quantify and interpret multiple
7089 sources of biological and technical variation in gene expression experiments.
7090 It uses a linear mixed model to quantify variation in gene expression
7091 attributable to individual, tissue, time point, or technical variables. The
7092 package includes dream differential expression analysis for repeated
7094 (license license:gpl2+)))
7096 (define-public r-htqpcr
7103 (uri (bioconductor-uri "HTqPCR" version))
7106 "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j"))))
7107 (properties `((upstream-name . "HTqPCR")))
7108 (build-system r-build-system)
7110 `(("r-affy" ,r-affy)
7111 ("r-biobase" ,r-biobase)
7112 ("r-gplots" ,r-gplots)
7113 ("r-limma" ,r-limma)
7114 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7115 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7116 "groups/bertone/software/HTqPCR.pdf"))
7117 (synopsis "Automated analysis of high-throughput qPCR data")
7119 "Analysis of Ct values from high throughput quantitative real-time
7120 PCR (qPCR) assays across multiple conditions or replicates. The input data
7121 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7122 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7123 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7124 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7125 loading, quality assessment, normalization, visualization and parametric or
7126 non-parametric testing for statistical significance in Ct values between
7127 features (e.g. genes, microRNAs).")
7128 (license license:artistic2.0)))
7130 (define-public r-unifiedwmwqpcr
7132 (name "r-unifiedwmwqpcr")
7137 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7140 "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81"))))
7142 `((upstream-name . "unifiedWMWqPCR")))
7143 (build-system r-build-system)
7145 `(("r-biocgenerics" ,r-biocgenerics)
7146 ("r-htqpcr" ,r-htqpcr)))
7147 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7148 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7150 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7151 data. This modified test allows for testing differential expression in qPCR
7153 (license license:gpl2+)))
7155 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7157 (define-public r-activedriverwgs
7159 (name "r-activedriverwgs")
7164 (uri (cran-uri "ActiveDriverWGS" version))
7167 "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
7169 `((upstream-name . "ActiveDriverWGS")))
7170 (build-system r-build-system)
7172 `(("r-biostrings" ,r-biostrings)
7173 ("r-bsgenome" ,r-bsgenome)
7174 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7175 ("r-genomeinfodb" ,r-genomeinfodb)
7176 ("r-genomicranges" ,r-genomicranges)
7177 ("r-iranges" ,r-iranges)
7179 ("r-s4vectors" ,r-s4vectors)))
7180 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7181 (synopsis "Driver discovery tool for cancer whole genomes")
7183 "This package provides a method for finding an enrichment of cancer
7184 simple somatic mutations (SNVs and Indels) in functional elements across the
7185 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7186 using whole genome sequencing data.")
7187 (license license:gpl3)))
7189 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7191 (define-public r-activepathways
7193 (name "r-activepathways")
7198 (uri (cran-uri "ActivePathways" version))
7201 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7203 `((upstream-name . "ActivePathways")))
7204 (build-system r-build-system)
7206 `(("r-data-table" ,r-data-table)
7207 ("r-ggplot2" ,r-ggplot2)))
7209 `(("r-knitr" ,r-knitr)))
7210 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7211 (synopsis "Multivariate pathway enrichment analysis")
7213 "This package represents an integrative method of analyzing multi omics
7214 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7215 uses a statistical data fusion approach, rationalizes contributing evidence
7216 and highlights associated genes, improving systems-level understanding of
7217 cellular organization in health and disease.")
7218 (license license:gpl3)))
7220 (define-public r-bgmix
7227 (uri (bioconductor-uri "BGmix" version))
7230 "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n"))))
7231 (properties `((upstream-name . "BGmix")))
7232 (build-system r-build-system)
7234 `(("r-kernsmooth" ,r-kernsmooth)))
7235 (home-page "https://bioconductor.org/packages/BGmix/")
7236 (synopsis "Bayesian models for differential gene expression")
7238 "This package provides fully Bayesian mixture models for differential
7240 (license license:gpl2)))
7242 (define-public r-bgx
7249 (uri (bioconductor-uri "bgx" version))
7252 "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx"))))
7253 (properties `((upstream-name . "bgx")))
7254 (build-system r-build-system)
7256 `(("r-affy" ,r-affy)
7257 ("r-biobase" ,r-biobase)
7258 ("r-gcrma" ,r-gcrma)
7259 ("r-rcpp" ,r-rcpp)))
7260 (home-page "https://bioconductor.org/packages/bgx/")
7261 (synopsis "Bayesian gene expression")
7263 "This package provides tools for Bayesian integrated analysis of
7264 Affymetrix GeneChips.")
7265 (license license:gpl2)))
7267 (define-public r-bhc
7274 (uri (bioconductor-uri "BHC" version))
7277 "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr"))))
7278 (properties `((upstream-name . "BHC")))
7279 (build-system r-build-system)
7280 (home-page "https://bioconductor.org/packages/BHC/")
7281 (synopsis "Bayesian hierarchical clustering")
7283 "The method implemented in this package performs bottom-up hierarchical
7284 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7285 in the data and Bayesian model selection to decide at each step which clusters
7286 to merge. This avoids several limitations of traditional methods, for example
7287 how many clusters there should be and how to choose a principled distance
7288 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7289 categories) or time-series data. This version also includes a randomised
7290 algorithm which is more efficient for larger data sets.")
7291 (license license:gpl3)))
7293 (define-public r-bicare
7300 (uri (bioconductor-uri "BicARE" version))
7303 "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y"))))
7304 (properties `((upstream-name . "BicARE")))
7305 (build-system r-build-system)
7307 `(("r-biobase" ,r-biobase)
7308 ("r-gseabase" ,r-gseabase)
7309 ("r-multtest" ,r-multtest)))
7310 (home-page "http://bioinfo.curie.fr")
7311 (synopsis "Biclustering analysis and results exploration")
7313 "This is a package for biclustering analysis and exploration of
7315 (license license:gpl2)))
7317 (define-public r-bifet
7324 (uri (bioconductor-uri "BiFET" version))
7327 "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5"))))
7328 (properties `((upstream-name . "BiFET")))
7329 (build-system r-build-system)
7331 `(("r-genomicranges" ,r-genomicranges)
7332 ("r-poibin" ,r-poibin)))
7334 `(("r-knitr" ,r-knitr)))
7335 (home-page "https://bioconductor.org/packages/BiFET")
7336 (synopsis "Bias-free footprint enrichment test")
7338 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7339 over-represented in target regions compared to background regions after
7340 correcting for the bias arising from the imbalance in read counts and GC
7341 contents between the target and background regions. For a given TF k, BiFET
7342 tests the null hypothesis that the target regions have the same probability of
7343 having footprints for the TF k as the background regions while correcting for
7344 the read count and GC content bias.")
7345 (license license:gpl3)))
7347 (define-public r-rsbml
7354 (uri (bioconductor-uri "rsbml" version))
7357 "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx"))))
7358 (properties `((upstream-name . "rsbml")))
7359 (build-system r-build-system)
7361 `(("libsbml" ,libsbml)
7364 `(("r-biocgenerics" ,r-biocgenerics)
7365 ("r-graph" ,r-graph)))
7367 `(("pkg-config" ,pkg-config)))
7368 (home-page "http://www.sbml.org")
7369 (synopsis "R support for SBML")
7371 "This package provides an R interface to libsbml for SBML parsing,
7372 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7373 (license license:artistic2.0)))
7375 (define-public r-hypergraph
7377 (name "r-hypergraph")
7382 (uri (bioconductor-uri "hypergraph" version))
7385 "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7"))))
7386 (properties `((upstream-name . "hypergraph")))
7387 (build-system r-build-system)
7389 `(("r-graph" ,r-graph)))
7390 (home-page "https://bioconductor.org/packages/hypergraph")
7391 (synopsis "Hypergraph data structures")
7393 "This package implements some simple capabilities for representing and
7394 manipulating hypergraphs.")
7395 (license license:artistic2.0)))
7397 (define-public r-hyperdraw
7399 (name "r-hyperdraw")
7404 (uri (bioconductor-uri "hyperdraw" version))
7407 "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf"))))
7408 (properties `((upstream-name . "hyperdraw")))
7409 (build-system r-build-system)
7410 (inputs `(("graphviz" ,graphviz)))
7412 `(("r-graph" ,r-graph)
7413 ("r-hypergraph" ,r-hypergraph)
7414 ("r-rgraphviz" ,r-rgraphviz)))
7415 (home-page "https://bioconductor.org/packages/hyperdraw")
7416 (synopsis "Visualizing hypergraphs")
7418 "This package provides functions for visualizing hypergraphs.")
7419 (license license:gpl2+)))
7421 (define-public r-biggr
7428 (uri (bioconductor-uri "BiGGR" version))
7431 "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk"))))
7432 (properties `((upstream-name . "BiGGR")))
7433 (build-system r-build-system)
7435 `(("r-hyperdraw" ,r-hyperdraw)
7436 ("r-hypergraph" ,r-hypergraph)
7438 ("r-limsolve" ,r-limsolve)
7439 ("r-rsbml" ,r-rsbml)
7440 ("r-stringr" ,r-stringr)))
7441 (home-page "https://bioconductor.org/packages/BiGGR/")
7442 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7444 "This package provides an interface to simulate metabolic reconstruction
7445 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7446 reconstruction databases. The package facilitates @dfn{flux balance
7447 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7448 networks and estimated fluxes can be visualized with hypergraphs.")
7449 (license license:gpl3+)))
7451 (define-public r-bigmemoryextras
7453 (name "r-bigmemoryextras")
7458 (uri (bioconductor-uri "bigmemoryExtras" version))
7461 "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g"))))
7463 `((upstream-name . "bigmemoryExtras")))
7464 (build-system r-build-system)
7466 `(("r-bigmemory" ,r-bigmemory)))
7468 `(("r-knitr" ,r-knitr)))
7469 (home-page "https://github.com/phaverty/bigmemoryExtras")
7470 (synopsis "Extension of the bigmemory package")
7472 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7473 safety and convenience features to the @code{filebacked.big.matrix} class from
7474 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7475 monitoring and gracefully restoring the connection to on-disk data and it also
7476 protects against accidental data modification with a filesystem-based
7477 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7478 classes as @code{assayData} matrices within the @code{Biobase} package's
7479 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7480 related to attaching to, and indexing into, file-backed matrices with
7481 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7482 a file-backed matrix with factor properties.")
7483 (license license:artistic2.0)))
7485 (define-public r-bigpint
7492 (uri (bioconductor-uri "bigPint" version))
7495 "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8"))))
7496 (properties `((upstream-name . "bigPint")))
7497 (build-system r-build-system)
7499 `(("r-delayedarray" ,r-delayedarray)
7500 ("r-dplyr" ,r-dplyr)
7501 ("r-ggally" ,r-ggally)
7502 ("r-ggplot2" ,r-ggplot2)
7503 ("r-gridextra" ,r-gridextra)
7504 ("r-hexbin" ,r-hexbin)
7505 ("r-hmisc" ,r-hmisc)
7506 ("r-htmlwidgets" ,r-htmlwidgets)
7507 ("r-plotly" ,r-plotly)
7509 ("r-rcolorbrewer" ,r-rcolorbrewer)
7510 ("r-reshape" ,r-reshape)
7511 ("r-shiny" ,r-shiny)
7512 ("r-shinycssloaders" ,r-shinycssloaders)
7513 ("r-shinydashboard" ,r-shinydashboard)
7514 ("r-stringr" ,r-stringr)
7515 ("r-summarizedexperiment" ,r-summarizedexperiment)
7516 ("r-tidyr" ,r-tidyr)))
7518 `(("r-knitr" ,r-knitr)))
7519 (home-page "https://github.com/lindsayrutter/bigPint")
7520 (synopsis "Big multivariate data plotted interactively")
7522 "This package provides methods for visualizing large multivariate
7523 datasets using static and interactive scatterplot matrices, parallel
7524 coordinate plots, volcano plots, and litre plots. It includes examples for
7525 visualizing RNA-sequencing datasets and differentially expressed genes.")
7526 (license license:gpl3)))
7528 (define-public r-chemminer
7530 (name "r-chemminer")
7535 (uri (bioconductor-uri "ChemmineR" version))
7538 "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf"))))
7539 (properties `((upstream-name . "ChemmineR")))
7540 (build-system r-build-system)
7542 `(("r-base64enc" ,r-base64enc)
7544 ("r-biocgenerics" ,r-biocgenerics)
7546 ("r-digest" ,r-digest)
7548 ("r-ggplot2" ,r-ggplot2)
7549 ("r-gridextra" ,r-gridextra)
7552 ("r-rcurl" ,r-rcurl)
7553 ("r-rjson" ,r-rjson)
7554 ("r-rsvg" ,r-rsvg)))
7556 `(("r-knitr" ,r-knitr)))
7557 (home-page "https://github.com/girke-lab/ChemmineR")
7558 (synopsis "Cheminformatics toolkit for R")
7560 "ChemmineR is a cheminformatics package for analyzing drug-like small
7561 molecule data in R. It contains functions for efficient processing of large
7562 numbers of molecules, physicochemical/structural property predictions,
7563 structural similarity searching, classification and clustering of compound
7564 libraries with a wide spectrum of algorithms. In addition, it offers
7565 visualization functions for compound clustering results and chemical
7567 (license license:artistic2.0)))
7569 (define-public r-bioassayr
7571 (name "r-bioassayr")
7576 (uri (bioconductor-uri "bioassayR" version))
7579 "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy"))))
7580 (properties `((upstream-name . "bioassayR")))
7581 (build-system r-build-system)
7583 `(("r-biocgenerics" ,r-biocgenerics)
7584 ("r-chemminer" ,r-chemminer)
7586 ("r-matrix" ,r-matrix)
7587 ("r-rjson" ,r-rjson)
7588 ("r-rsqlite" ,r-rsqlite)
7591 `(("r-knitr" ,r-knitr)))
7592 (home-page "https://github.com/TylerBackman/bioassayR")
7593 (synopsis "Cross-target analysis of small molecule bioactivity")
7595 "bioassayR is a computational tool that enables simultaneous analysis of
7596 thousands of bioassay experiments performed over a diverse set of compounds
7597 and biological targets. Unique features include support for large-scale
7598 cross-target analyses of both public and custom bioassays, generation of
7599 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7600 preloaded database that provides access to a substantial portion of publicly
7601 available bioactivity data.")
7602 (license license:artistic2.0)))
7604 (define-public r-biobroom
7611 (uri (bioconductor-uri "biobroom" version))
7614 "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf"))))
7615 (properties `((upstream-name . "biobroom")))
7616 (build-system r-build-system)
7618 `(("r-biobase" ,r-biobase)
7619 ("r-broom" ,r-broom)
7620 ("r-dplyr" ,r-dplyr)
7621 ("r-tidyr" ,r-tidyr)))
7623 `(("r-knitr" ,r-knitr)))
7624 (home-page "https://github.com/StoreyLab/biobroom")
7625 (synopsis "Turn Bioconductor objects into tidy data frames")
7627 "This package contains methods for converting standard objects
7628 constructed by bioinformatics packages, especially those in Bioconductor, and
7629 converting them to @code{tidy} data. It thus serves as a complement to the
7630 @code{broom} package, and follows the same tidy, augment, glance division of
7631 tidying methods. Tidying data makes it easy to recombine, reshape and
7632 visualize bioinformatics analyses.")
7633 ;; Any version of the LGPL.
7634 (license license:lgpl3+)))
7636 (define-public r-graphite
7643 (uri (bioconductor-uri "graphite" version))
7646 "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p"))))
7647 (properties `((upstream-name . "graphite")))
7648 (build-system r-build-system)
7650 `(("r-annotationdbi" ,r-annotationdbi)
7651 ("r-checkmate" ,r-checkmate)
7652 ("r-graph" ,r-graph)
7654 ("r-rappdirs" ,r-rappdirs)))
7655 (home-page "https://bioconductor.org/packages/graphite/")
7656 (synopsis "Networks from pathway databases")
7658 "Graphite provides networks derived from eight public pathway databases,
7659 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7661 (license license:agpl3+)))
7663 (define-public r-reactomepa
7665 (name "r-reactomepa")
7670 (uri (bioconductor-uri "ReactomePA" version))
7673 "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x"))))
7674 (properties `((upstream-name . "ReactomePA")))
7675 (build-system r-build-system)
7677 `(("r-annotationdbi" ,r-annotationdbi)
7679 ("r-enrichplot" ,r-enrichplot)
7680 ("r-ggplot2" ,r-ggplot2)
7681 ("r-ggraph" ,r-ggraph)
7682 ("r-graphite" ,r-graphite)
7683 ("r-igraph" ,r-igraph)
7684 ("r-reactome-db" ,r-reactome-db)))
7686 `(("r-knitr" ,r-knitr)))
7687 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7688 (synopsis "Reactome pathway analysis")
7690 "This package provides functions for pathway analysis based on the
7691 REACTOME pathway database. It implements enrichment analysis, gene set
7692 enrichment analysis and several functions for visualization.")
7693 (license license:gpl2)))
7695 (define-public r-ebarrays
7702 (uri (bioconductor-uri "EBarrays" version))
7705 "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf"))))
7706 (properties `((upstream-name . "EBarrays")))
7707 (build-system r-build-system)
7709 `(("r-biobase" ,r-biobase)
7710 ("r-cluster" ,r-cluster)
7711 ("r-lattice" ,r-lattice)))
7712 (home-page "https://bioconductor.org/packages/EBarrays/")
7713 (synopsis "Gene clustering and differential expression identification")
7715 "EBarrays provides tools for the analysis of replicated/unreplicated
7717 (license license:gpl2+)))
7719 (define-public r-bioccasestudies
7721 (name "r-bioccasestudies")
7726 (uri (bioconductor-uri "BiocCaseStudies" version))
7729 "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix"))))
7731 `((upstream-name . "BiocCaseStudies")))
7732 (build-system r-build-system)
7733 (propagated-inputs `(("r-biobase" ,r-biobase)))
7734 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7735 (synopsis "Support for the case studies monograph")
7737 "This package provides software and data to support the case studies
7739 (license license:artistic2.0)))
7741 (define-public r-biocgraph
7743 (name "r-biocgraph")
7748 (uri (bioconductor-uri "biocGraph" version))
7751 "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj"))))
7752 (properties `((upstream-name . "biocGraph")))
7753 (build-system r-build-system)
7755 `(("r-biocgenerics" ,r-biocgenerics)
7756 ("r-geneplotter" ,r-geneplotter)
7757 ("r-graph" ,r-graph)
7758 ("r-rgraphviz" ,r-rgraphviz)))
7759 (home-page "https://bioconductor.org/packages/biocGraph/")
7760 (synopsis "Graph examples and use cases in Bioinformatics")
7762 "This package provides examples and code that make use of the
7763 different graph related packages produced by Bioconductor.")
7764 (license license:artistic2.0)))
7766 (define-public r-experimenthub
7768 (name "r-experimenthub")
7773 (uri (bioconductor-uri "ExperimentHub" version))
7776 "18d6kjfavy5b769gpkblihdkz2nz2hsgyjki8mp1sywi0ik08ncd"))))
7777 (properties `((upstream-name . "ExperimentHub")))
7778 (build-system r-build-system)
7780 `(("r-annotationhub" ,r-annotationhub)
7781 ("r-biocfilecache" ,r-biocfilecache)
7782 ("r-biocgenerics" ,r-biocgenerics)
7783 ("r-biocmanager" ,r-biocmanager)
7785 ("r-rappdirs" ,r-rappdirs)
7786 ("r-s4vectors" ,r-s4vectors)))
7788 `(("r-knitr" ,r-knitr)))
7789 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7790 (synopsis "Client to access ExperimentHub resources")
7792 "This package provides a client for the Bioconductor ExperimentHub web
7793 resource. ExperimentHub provides a central location where curated data from
7794 experiments, publications or training courses can be accessed. Each resource
7795 has associated metadata, tags and date of modification. The client creates
7796 and manages a local cache of files retrieved enabling quick and reproducible
7798 (license license:artistic2.0)))
7800 (define-public r-multiassayexperiment
7802 (name "r-multiassayexperiment")
7807 (uri (bioconductor-uri "MultiAssayExperiment" version))
7810 "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh"))))
7812 `((upstream-name . "MultiAssayExperiment")))
7813 (build-system r-build-system)
7815 `(("r-biobase" ,r-biobase)
7816 ("r-biocgenerics" ,r-biocgenerics)
7817 ("r-genomicranges" ,r-genomicranges)
7818 ("r-iranges" ,r-iranges)
7819 ("r-s4vectors" ,r-s4vectors)
7820 ("r-summarizedexperiment" ,r-summarizedexperiment)
7821 ("r-tidyr" ,r-tidyr)))
7823 `(("r-knitr" ,r-knitr)))
7824 (home-page "https://waldronlab.io/MultiAssayExperiment/")
7825 (synopsis "Integration of multi-omics experiments in Bioconductor")
7827 "MultiAssayExperiment harmonizes data management of multiple assays
7828 performed on an overlapping set of specimens. It provides a familiar
7829 Bioconductor user experience by extending concepts from
7830 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7831 classes for individual assays, and allowing subsetting by genomic ranges or
7833 (license license:artistic2.0)))
7835 (define-public r-bioconcotk
7837 (name "r-bioconcotk")
7842 (uri (bioconductor-uri "BiocOncoTK" version))
7845 "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk"))))
7846 (properties `((upstream-name . "BiocOncoTK")))
7847 (build-system r-build-system)
7849 `(("r-bigrquery" ,r-bigrquery)
7851 ("r-complexheatmap" ,r-complexheatmap)
7852 ("r-curatedtcgadata" ,r-curatedtcgadata)
7854 ("r-dplyr" ,r-dplyr)
7856 ("r-genomicfeatures" ,r-genomicfeatures)
7857 ("r-genomicranges" ,r-genomicranges)
7858 ("r-ggplot2" ,r-ggplot2)
7859 ("r-ggpubr" ,r-ggpubr)
7860 ("r-graph" ,r-graph)
7862 ("r-iranges" ,r-iranges)
7863 ("r-magrittr" ,r-magrittr)
7865 ("r-rgraphviz" ,r-rgraphviz)
7866 ("r-rjson" ,r-rjson)
7867 ("r-s4vectors" ,r-s4vectors)
7868 ("r-scales" ,r-scales)
7869 ("r-shiny" ,r-shiny)
7870 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7872 `(("r-knitr" ,r-knitr)))
7873 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7874 (synopsis "Bioconductor components for general cancer genomics")
7876 "The purpose of this package is to provide a central interface to various
7877 tools for genome-scale analysis of cancer studies.")
7878 (license license:artistic2.0)))
7880 (define-public r-biocor
7887 (uri (bioconductor-uri "BioCor" version))
7890 "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy"))))
7891 (properties `((upstream-name . "BioCor")))
7892 (build-system r-build-system)
7894 `(("r-biocparallel" ,r-biocparallel)
7895 ("r-gseabase" ,r-gseabase)
7896 ("r-matrix" ,r-matrix)))
7898 `(("r-knitr" ,r-knitr)))
7899 (home-page "https://llrs.github.io/BioCor/")
7900 (synopsis "Functional similarities")
7902 "This package provides tools to calculate functional similarities based
7903 on the pathways described on KEGG and REACTOME or in gene sets. These
7904 similarities can be calculated for pathways or gene sets, genes, or clusters
7905 and combined with other similarities. They can be used to improve networks,
7906 gene selection, testing relationships, and so on.")
7907 (license license:expat)))
7909 (define-public r-biocpkgtools
7911 (name "r-biocpkgtools")
7916 (uri (bioconductor-uri "BiocPkgTools" version))
7919 "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr"))))
7920 (properties `((upstream-name . "BiocPkgTools")))
7921 (build-system r-build-system)
7923 `(("r-biocfilecache" ,r-biocfilecache)
7924 ("r-biocmanager" ,r-biocmanager)
7925 ("r-biocviews" ,r-biocviews)
7926 ("r-dplyr" ,r-dplyr)
7929 ("r-graph" ,r-graph)
7930 ("r-htmltools" ,r-htmltools)
7931 ("r-htmlwidgets" ,r-htmlwidgets)
7933 ("r-igraph" ,r-igraph)
7934 ("r-jsonlite" ,r-jsonlite)
7935 ("r-magrittr" ,r-magrittr)
7936 ("r-rappdirs" ,r-rappdirs)
7938 ("r-readr" ,r-readr)
7940 ("r-rlang" ,r-rlang)
7941 ("r-rvest" ,r-rvest)
7942 ("r-stringr" ,r-stringr)
7943 ("r-tibble" ,r-tibble)
7944 ("r-tidyr" ,r-tidyr)
7945 ("r-tidyselect" ,r-tidyselect)
7946 ("r-xml2" ,r-xml2)))
7948 `(("r-knitr" ,r-knitr)))
7949 (home-page "https://github.com/seandavi/BiocPkgTools")
7950 (synopsis "Collection of tools for learning about Bioconductor packages")
7952 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7953 and build status. This package is a simple collection of functions to access
7954 that metadata from R. The goal is to expose metadata for data mining and
7955 value-added functionality such as package searching, text mining, and
7956 analytics on packages.")
7957 (license license:expat)))
7959 (define-public r-biocset
7966 (uri (bioconductor-uri "BiocSet" version))
7969 "14dmkc878lskbm001kgjyqmrwnn6s032z4h64f617f1xd9zx9wrj"))))
7970 (properties `((upstream-name . "BiocSet")))
7971 (build-system r-build-system)
7973 `(("r-annotationdbi" ,r-annotationdbi)
7974 ("r-dplyr" ,r-dplyr)
7975 ("r-keggrest" ,r-keggrest)
7977 ("r-rlang" ,r-rlang)
7978 ("r-rtracklayer" ,r-rtracklayer)
7979 ("r-tibble" ,r-tibble)))
7981 `(("r-knitr" ,r-knitr)))
7983 "https://bioconductor.org/packages/BiocSet")
7985 "Representing Different Biological Sets")
7987 "BiocSet displays different biological sets in a triple tibble format.
7988 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
7989 The user has the ability to activate one of these three tibbles to perform
7990 common functions from the @code{dplyr} package. Mapping functionality and
7991 accessing web references for elements/sets are also available in BiocSet.")
7992 (license license:artistic2.0)))
7994 (define-public r-biocworkflowtools
7996 (name "r-biocworkflowtools")
8001 (uri (bioconductor-uri "BiocWorkflowTools" version))
8004 "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy"))))
8006 `((upstream-name . "BiocWorkflowTools")))
8007 (build-system r-build-system)
8009 `(("r-biocstyle" ,r-biocstyle)
8010 ("r-bookdown" ,r-bookdown)
8011 ("r-git2r" ,r-git2r)
8013 ("r-knitr" ,r-knitr)
8014 ("r-rmarkdown" ,r-rmarkdown)
8015 ("r-rstudioapi" ,r-rstudioapi)
8016 ("r-stringr" ,r-stringr)
8017 ("r-usethis" ,r-usethis)))
8019 `(("r-knitr" ,r-knitr)))
8020 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8021 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8023 "This package provides functions to ease the transition between
8024 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8025 (license license:expat)))
8027 (define-public r-biodist
8034 (uri (bioconductor-uri "bioDist" version))
8037 "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp"))))
8038 (properties `((upstream-name . "bioDist")))
8039 (build-system r-build-system)
8041 `(("r-biobase" ,r-biobase)
8042 ("r-kernsmooth" ,r-kernsmooth)))
8043 (home-page "https://bioconductor.org/packages/bioDist/")
8044 (synopsis "Different distance measures")
8046 "This package provides a collection of software tools for calculating
8047 distance measures.")
8048 (license license:artistic2.0)))
8050 (define-public r-pcatools
8057 (uri (bioconductor-uri "PCAtools" version))
8060 "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc"))))
8061 (properties `((upstream-name . "PCAtools")))
8062 (build-system r-build-system)
8064 `(("r-beachmat" ,r-beachmat)
8066 ("r-biocparallel" ,r-biocparallel)
8067 ("r-biocsingular" ,r-biocsingular)
8068 ("r-cowplot" ,r-cowplot)
8069 ("r-delayedarray" ,r-delayedarray)
8070 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8071 ("r-dqrng" ,r-dqrng)
8072 ("r-ggplot2" ,r-ggplot2)
8073 ("r-ggrepel" ,r-ggrepel)
8074 ("r-lattice" ,r-lattice)
8075 ("r-matrix" ,r-matrix)
8077 ("r-reshape2" ,r-reshape2)))
8078 (native-inputs `(("r-knitr" ,r-knitr)))
8079 (home-page "https://github.com/kevinblighe/PCAtools")
8080 (synopsis "PCAtools: everything Principal Components Analysis")
8082 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8083 structure of the data without the need to build any model to represent it.
8084 This \"summary\" of the data is arrived at through a process of reduction that
8085 can transform the large number of variables into a lesser number that are
8086 uncorrelated (i.e. the 'principal components'), while at the same time being
8087 capable of easy interpretation on the original data. PCAtools provides
8088 functions for data exploration via PCA, and allows the user to generate
8089 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8090 can also identify an optimal number of principal components via different
8091 metrics, such as the elbow method and Horn's parallel analysis, which has
8092 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8093 dimensional mass cytometry data.")
8094 (license license:gpl3)))
8096 (define-public r-rgreat
8103 (uri (bioconductor-uri "rGREAT" version))
8106 "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
8107 (properties `((upstream-name . "rGREAT")))
8108 (build-system r-build-system)
8110 `(("r-genomicranges" ,r-genomicranges)
8111 ("r-getoptlong" ,r-getoptlong)
8112 ("r-iranges" ,r-iranges)
8113 ("r-rcurl" ,r-rcurl)
8114 ("r-rjson" ,r-rjson)))
8115 (native-inputs `(("r-knitr" ,r-knitr)))
8116 (home-page "https://github.com/jokergoo/rGREAT")
8117 (synopsis "Client for GREAT analysis")
8119 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8120 Tool) analysis automatic by constructing a HTTP POST request according to
8121 user's input and automatically retrieving results from GREAT web server.")
8122 (license license:expat)))
8124 (define-public r-m3c
8131 (uri (bioconductor-uri "M3C" version))
8134 "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
8135 (properties `((upstream-name . "M3C")))
8136 (build-system r-build-system)
8138 `(("r-cluster" ,r-cluster)
8139 ("r-corpcor" ,r-corpcor)
8140 ("r-doparallel" ,r-doparallel)
8141 ("r-dosnow" ,r-dosnow)
8142 ("r-foreach" ,r-foreach)
8143 ("r-ggplot2" ,r-ggplot2)
8144 ("r-matrix" ,r-matrix)
8145 ("r-matrixcalc" ,r-matrixcalc)
8146 ("r-rtsne" ,r-rtsne)
8147 ("r-umap" ,r-umap)))
8148 (native-inputs `(("r-knitr" ,r-knitr)))
8149 (home-page "https://bioconductor.org/packages/M3C")
8150 (synopsis "Monte Carlo reference-based consensus clustering")
8152 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8153 simulation to eliminate overestimation of @code{K} and can reject the null
8154 hypothesis @code{K=1}.")
8155 (license license:agpl3+)))